130 File Reference

Generated from nmhelp plain-text source files (*.fil) of the NONMEM 7.6.0 distribution. These mirror the content presented by nmhelp and complement the formatted Part VIII Help Guide.

1 ADDITIONAL_OUTPUT_FILES

MEANING: NONMEM Additional Output files

CONTEXT: NONMEM Output Files

DISCUSSION:

With NONMEM 7, a NONMEM run produces several additional output files. These provide a more efficient way of extracting numerical results from the analysis than by obtaining them from the NONMEM report file. (See raw_output_file).

Names of the files start with “root”, where root is the root name (not including extension) of the NM-TRAN control stream file given at the nmfe command line, or root=“nmbayes” if the control stream file name is not passed as an argument to the NONMEM executable. In this example the root is myexample, and NONMEM 7.5 is invoked. nmfe75 myexample.ctl myexample.res The files have names with extensions (suffixes) .ext, .cov, .clt, .coi, .cor, .cpu, .phi, .phm, .grd, .shk, .shm, .cnv, smt, .rmt, .vpd, .ets, .bfm. In this example, they will be myexample.cov, myexample.coi, etc.

Each type of file accumulates information from each step that generates the type of output in question.

The first two lines of each file is the same. First is a header line that begins with the word TABLE, such as:

TABLE NO. n:

These tables are not related to the ones produced by the $TABLE record. The value of n is incremented each time the Estimation Step is implemented, i.e., once per $ESTIM record, when MAXEVAL is not 0 and $EST is not omitted. The $EST records may be in the same problem, or in subsequent problems. If $COV is present in a problem without $EST (e.g., when $MSFI is used), then n is also incremented.

Next on the header line is the analysis text (same as given on the #METH: line in the report file), e.g., “First Order”.

Also on this line are:

Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0: Superproblem2=0 Iteration2=0

The values of Problem, Subproblem, Superproblem1, Iteration1, Superproblem2, Iteration2 are the same values as would be found in the following variables in modules during the run: IPROB IREP S1NUM S1IT S2NUM S2IT

The second line contains the column headers for the current additional file, all on one line.

Options NOTITLE and NOLABEL and FORMAT of the $ESTIMATION record can be used to supress the first and/or second lines, and to modify the format of the values in the table. They apply to raw and additional output files, but only for the current Estimation Step. The options must be re-specified with each $EST record.

The additional output files are:

root.ext: Always. (See raw_output_file).
root.phi: Always. Individual phi parameters (phi(i)=mu(i)+eta(i), for ith parameter), and their variances phc(,). For parameters not MU referenced phi(i)=eta(i). When a classical method is performed (FOCE, Laplace), then mode of posterior eta(i) are printed out, along with their Fisher information (first order expected value for FOCE, second order for Laplace) assessed variances etc(,). For ITS, these parameters are the modes of the posterior density, with first-order approximated expected variances (or second order variances if $EST METHOD=ITS LAPLCE is used). For IMP, IMPMAP, SAEM methods, they are the Monte Carlo evaluated conditional mean parameters and variances of the parameters under the posterior density. For MCMC Bayesian, they are random single samples of phi(), as of the last position. Their variances are zero. Individual objective function values (obji) are also produced. As of NONMEM 7.4, if $EST PHITYPE=1 is specified, then conditional mean etas are reported in the phi table. regardless of the analysis method.
root.iph (NM75): As of nm75, samples of phi/eta are collected at each BAYES iteration, and summarized to provide conditional mean phi and phc() in the root.phi table, as described above. By default, the individual phi values from each iteration are not stored. However, if you set $EST … BAYES_PHI_STORE=1 then phi and eta values from each BAYES iteration will be stored in root.iph. For non-mixture problems, only records of SUBP=0 are recorded, as there are no sub-population divisions. For mixture problems, the SUBP=0 records contain the composite phis and etas (the average of these across all non-negative iterations are in the root.phi table), and the SUBP>0 records contain the phis and etas appropriate to each sub-population SUBP (the average of these across all non- negative iterations are in the root.phm table). The root.iph file can become quite large, so it should be used only on the final analysis.
root.phm (NM72): Individual phi/eta/obji parameters per sub-population. This file is only produced in $MIXTURE problems. As of nm75, for MCMC Baysian analysis, the items listed in this table consist of the average values among all the iterations during the stationary distribution phase. Before nm75, the values consisted of values from the last MCMC iteration.
root.shk (NM72): This file presents composite eta shrinkage and epsilon shrinkage information, the same as given in the NONMEM report file between the #TERM: and #TERE: tags, but in rows/column format, and with adjustable formatting. (See shrinkage).
root.shm (NM73): This file is a shrinkage map describing which etas were included or excluded in the eta shrinkage assessment. (See shrinkage).
root.grd (NM72): Gradient values for classical NONMEM methods. Always.
root.xml (NM72): An XML markup version of the contents of the NONMEM report file. The rules by which it is constructed are given in output.xsd and output.dtd.
root.cov: Full variance-covariance error matrix of thetas, sigmas, and omegas. Same as “COVARIANCE MATRIX OF ESTIMATE” in the NONMEM report except that it is full (NONMEM displays only the lower triangle), elements that are fixed or not estimated are displayed as 0 (NONMEM displays them as …..), and, when the data are individual, sigma is displayed as 0 (NONMEM does not display sigma at all.) Only generated if the $COVARIANCE record is present. (See covariance matrix of estimate). (See Covariance_Output_files). (See order_option).
root.clt (NM74): The lower-triangular portion of the variance-covariance of the parameter estimates reported in root.cov. This is provided for easier pasting of the information as theta priors for a subsequent analysis. Only generated if the $COVARIANCE record is present.
root.cor: Full correlation matrix of thetas, sigmas, and omegas. Same as “CORRELATION MATRIX OF ESTIMATE”, except as described for root.cov. (See correlation matrix of estimate).
root.coi: Full inverse covariance matrix (Fischer information matrix) for thetas, sigmas, and omegas. Same as “INVERSE COVARIANCE MATRIX OF ESTIMATE” except as described for root.cov.
root.cnv (NM72): Convergence information for the Monte Carlo/EM methods, if CTYPE>0. (See raw_output_file).
root.smt (NM72): Contains the S matrix, if $COV step failed.
root.rmt (NM72): Contains the R matrix, if $COV step failed.
root.imp (NM73): Produced if the user selects importance sampling with option IACCEPT=0.0. Contains the final IACCEPT and DF values that NONMEM selected for each subject.
root.npd (NM73): For NONPARAMETRIC method. Each row contains information about a support point.
root.npe (NM73): For NONPARAMETRIC method. The expected value etas and expected value eta covariances (ETC) are listed for each problem or subproblem.
root.npi (NM73): For NONPARAMETRIC method. The individual probabilities are listed. Each row contains information about a support point.
root.npl (NM74): For NONPARAMETRIC method. The individual data likelihoods (not including the parameter density) are listed in this file.
root.fgh (NM73): This file is produced if the user selects $EST NUMDER=1 or NUMDER=3. The file lists the numerically evaluated derivatives of Y with respect to eta, where F=Y (the prediction) G(I,1)=partial Y with respect to eta(i)) G(I,J+1)=Second derivatives of Y with respect to eta(i),eta(j) H(I,1)=partial Y with respect to eps(i) H(i,j+1)=partial Y with respect to eps(i),eta(j) The values are those used in the Estimation Step. Values of F are computed by PRED with eta=0 if METHOD=0 is used; otherwise they are computed with non-zero etas: the Conditional (CPE) etas, empirical bayes estimates (EBE), mode a posteriori (MAP) estimates) or conditional mean etas, depending on the Estimation Method. Values of G are computed by NONMEM via finite differences using these values of F and eta. Values of H are computed by NONMEM with the same values of F and eta if INTERACTION is specified; otherwise, they are computed with eta=0.
root.agh (NM73): This file is produced if the user selects $EST NUMDER=2 or NUMDER=3. The file lists the analytically evaluated derivatives of Y with respect to eta. The format and order is the same as file root.fgh. The values are those returned by subroutine PRED in arguments F, G, and H. These are 0 if not computed by PRED. (E.g. second derivatves are not computed analytically with a method other than LAPLACIAN.) Values in root.agh correspond exactly to those in root.fgh. That is, values of F and G are from calls to PRED with eta=0 or with non-zero etas, as described above. Values of H are from calls to PRED with the same values of eta if INTERACTION is specified; otherwise, they are from calls to PRED with eta=0, regardless of the Estimation method.
root.vpd (NM74): This file is produced if the $TABLE file option VARCALC=1 or VARCALC=2 is used. It is the full variances- covariances among all user-defined and PREDPP parameters. The FORMAT used for this file is that defined in the $EST record.
root.ets (NM74): As of NM74, one can obtain random samples of individual etas, and uses these for covariate and model diagnostics. $EST option ETASAMPLES=1 causes individual ISAMPLE random eta samples per subject, to be written to root.ets, where root is the root name of the control stream file. See “Stochastic Approximation Expectation Maximization (SAEM) Method” in Guide Introduction_7.
root.bfm (NM75): When OFVTYPE=8 during optimal design ($DESIGN OFVTYPE=8) the progress of average individual conditional variances (average empirical Bayes conditional variance) are shown in the root.bfm file (where root is name of control stream file), and the final one on the -1000000000 line, during an optimization. The RAW file (by default named root.ext) which shows only the starting, and final values of the standard errors of population parameters, as extra information.
root.cpu (NM73): The cpu time in seconds is reported in this file. It is an accurate representation of the computer usage, whether single or parallel process. The same problem when run singly or in parallel will report a similar cpu time. This is in contrast with elapsed time, which is improved with parallelization.

With NONMEM 7.3 and higher, the $THETAI and $THETAR records may be used to transform initial and final estimates of THETA, respectively. This will affect values in the .ext, .cov, etc. files (See $thetai, $thetar)

REFERENCES: Guide Introduction_7

2 MODEL SPECIFICATION FILE

MEANING: A NONMEM output and input file

CONTEXT: NONMEM input/output file

DISCUSSION:

A Model Specification File (MSF) can be output by NONMEM. It includes information from the Estimation Step (initial estimate information, current (or final) estimate information, search information) and from the Covariance Step (if this step is implemented). It is requested in a certain field of the ESTIMATION control record (or, with NM-TRAN, by an option of the $ESTIMATION record). NONMEM will use the information in the MSF in a later problem, either to continue the parameter search if the search did not terminate in the current run, or to perform other tasks that will be based on final parameter estimates in the MSF. These other tasks can be Simulation, Covariance, Table, Scatterplot, or Finalization Steps. If the MSF contains the results of a search that terminated successfully, even an additional Estimation Step can be performed, using the final parameter estimates in the MSF as initial estimates and an estimation method other than the one used in the problem with which the MSF was output. If an MSF is output, and intermediate output with iteration summaries is requested, then NONMEM also writes the parameter estimates of these summaries to file INTER.

MSF files are often used because they eliminate needless duplication of computation that has already occurred in the Estimation Step of a previous run. If there should be a computer crash during or after the Estimation Step of the previous run and a MSF was output, then with the current run, the MSF can be input, and the Estimation Step of the current run will continue the search begun with the previous run, starting from the last iteration whose summary was output before the crash occurred.

With NM-TRAN, specification that an existing Model Specification File is to be input is done by placing the file’s name on the $MSFI record.

With NONMEM 7.3, when MSF or MSFO option is used to specify an MSFO file in the $EST record e.g., $EST … MSFO=msfroot.msf then in addition to the main MSF file msfroot.msf, an extra file msfroot_ETAS.msf will also be produced, and provide additional information when a $MSFI record is used in a subsequent problem or control stream. File msfroot_ETAS.msf contains individual etas and phis generated during estimation (except FO method, which does not generate non-zero etas during estimation, and not POSTHOC evaluated etas.) The use of an extension in the file name, e.g., .msf, is optional. If file _ETAS does not exist, NONMEM issues a warning, e.g.,

WARNING: EXTRA MSF FILE COULD NOT BE OPENED: c5msf2x_ETAS

If the Covariance Step is also implemented, extra files msfroot_RMAT.msf and msfroot_SMAT.msf containing intermediate information on the R matrix and S matrix will also be produced. These files provide information when a $MSFI record along with a $COV … RESUME record is used in a subsequent problem or control stream. There is no warning if files _SMAT and/or _RMAT are missing.

EXAMPLE OF USAGE:

Here is an example using NM-TRAN. A fragment of the control stream for the first run follows. The Estimation Step is run for a limited number of evaluations of the objective function (200).

$THETA  (.1,3,5) (.008,.08,.5) (.004,.04,.9)
$OMEGA BLOCK(3)  6 .005 .0002 .3 .006 .4
$SIGMA  .4
$EST     MAXEVAL=200  PRINT=5 MSFO=msf1

After review of the first run’s output, it is decided to let the search continue. The continuation will start from the iteration during which the 200th objective function evaluation occurred in the previous search. A fragment of the control stream for the second run follows. $THETA, $OMEGA, and $SIGMA need not, and may not, be present. The Estimation Step is allowed to run to completion, and standard errors and a table are requested. A new MSF is obtained, which will allow additional tables and scatterplots to be obtained later.

$MSFI msf1
$EST PRINT=5 MSFO=msf2
$COV
$TABLE ID TIME

REFERENCES: Guide I, section B.3; Guide IV, section III.B.12

3 NM-TRAN OUTPUT FILES

MEANING: NM-TRAN output files

CONTEXT: NONMEM input file

DISCUSSION:

NM-TRAN produces several output files, several of which are input files to NONMEM itself.

In the first column, the files are listed by the default file names supplied by constants in NM-TRAN’s ABLOCK routine. (Some installations may use different names for these files.)

The second column lists the inputs to NM-TRAN that contribute to these files.

The third column indicates how the files are used.

Note that file FSIZES is a convenient reference for users to view, but is not used. SUBROUTINE FSIZESR in FSUBS is what is actually used during the NONMEM run.

File Relevant portion How file is used name of NM-TRAN inputs

FCON All NONMEM (control stream) FDATA Data file, $DATA, $INPUT NONMEM (data file)

FSTREAM Filenames from $DATA, NONMEM (file control stream)

$MSFI, $MSFO, $TABLE

FSUBS Abbreviated code Generated FORTRAN subroutines

FREPORT $SUBROUTINES Input to whatever generates: the commands that create the NONMEM executable (e.g., the NMLINK routine).
FORIG Abbreviated code, $ABBR When $ABBR REPLACE is used,: this file contains the original abbreviated code.
FREPL Abbreviated code, $ABBR When $ABBR REPLACE is used,: this file contains the postreplacement abbreviated code.

FWORK Data file NM-TRAN (work file)

FWARN All Warning and informational: messages.

FSIZES Abbreviated code, Dynamic array sizes for NON-

$THETA, $OMEGA,  $SIGMA,   MEM
$SIZES, SIZES.f90

prsizes Abbreviated code, Static array sizes for PREDPP

$THETA,  $OMEGA, $SIGMA,
$SIZES, SIZES.f90

With NONMEM 7, files FSUBS2 and FSUBS_MU are used by NMTRAN as work files during the creation of FSUBS.

REFERENCES: Guide III, section V.6.0; Guide Introduction_7

4 NONMEM CONTROL STREAM

MEANING: NONMEM control records

CONTEXT: NONMEM input file

DISCUSSION:

NONMEM control records contain the instructions to NONMEM. The set of control records is called the NONMEM control stream. These are different from NM-TRAN control records.

When NM-TRAN is used, NM-TRAN creates the NONMEM control stream in a file named FCON. When NM-TRAN is not used, the user must create it himself.

Each NONMEM control record begins with a 3 or 4-character preface (record label) which identifies the record. They are listed here in the same order in which they must appear in the NONMEM control stream. For details of the contents of the records, see NONMEM Users Guide V “Introductory Guide”, Appendix 4 - NONMEM Control Records (FCON).

Record type Prefix Corresponding NM-TRAN record

 FILE                           FILE     none
 SUPER PROBLEM                  SUPR     $SUPER
 PROBLEM                        PROB     $PROBLEM
 DEFAULT                        DFLT     $DEFAULT

Data set specification records

 DATA                           DATA     $DATA
 ITEM                           ITEM     $INPUT
 INDEX                          INDX     $INDEX
 LABEL                          LABL     $INPUT,$TABLE,$SCATTER
 EXTRA EVID                     XVID     $INPUT
 FORMAT                         FORM     $DATA

Model specification records
FIND                           FIND     $MSFI
VERSION                        MSFV     $MSFI
STRUCTURE                      STRC     $THETA, $OMEGA, $SIGMA
LEVEL                          OLEV     $LEVEL

Initial estimate records THETA CONSTRAINT THCN $THETA

 THETA                          THTA     $THETA
 LOWER BOUND                    LOWR     $THETA
 UPPER BOUND                    UPPR     $THETA
 DIAGONAL                       DIAG     $OMEGA, $SIGMA
 BLOCK SET                      BLST     $OMEGA, $SIGMA
 ETA VALUES                     ETA      $ETAS
 PHI VALUES                     PHI      $PHIS
 CHAIN                          CHN      $CHAIN
 CHAIN FILE                     CFIL     $CHAIN
 CHAIN DELIMITER                CDLM     $CHAIN
 CHAIN Order                    ORDR     $CHAIN
 CHAIN PARAFILE                 CHFL     $CHAIN (not used)
 OMEGA VALUES                   ANNL     $ANNEAL

Task specification records
SIMULATION                     SIML     $SIMULATION
RANDOM SOURCE                  SORC     $SIMULATION
SIMULATION PARAFILE            SFIL     $SIMULATION
ESTIMATION                     ESTM     $ESTIMATION
ESTIMATION                     BEST     $ESTIMATION
ESTIMATION PARAFILE            BFIL     $ESTIMATION
ESTIMATION PARAFILE            PFIL     $ESTIMATION
ESTIMATION FPARAFILE           FFIL     $ESTIMATION
ZERO                           ZERO     $ESTIMATION
OMIT                           OMIT     $OMIT
ESTIMATION GRID                GRID     $ESTIMATION
NONPARAMETRIC                  NONP     $NONPARAMETRIC
COVARIANCE                     COVR     $COVARIANCE
COVARIANCE                     COVT     $COVARIANCE
COVARIANCE PARAFILE            CPAR     $COVARIANCE
COVARIANCE SIRPARAFILE         SPAR     $COVARIANCE
TABLE                          TABL     $TABLE
TABLE PARAFILE                 PPAR     $TABLE
SCATTERPLOT                    SCAT     $SCATTERPLOT
Output specification records
ESTIMATION DELIMITER           BDLM     $ESTIMATION
ESTIMATION MUM                 BMUM     $ESTIMATION
ESTIMATION GRD                 BGRD     $ESTIMATION
ESTIMATION ORDER               ORDR     $ESTIMATION
LFORMAT                        FRML     $TABLE
RFORMAT                        FRMR     $TABLE
ADDITIONAL DIAGNOSTIC LABELS   LBW1     $TABLE,$SCATTER
SYMBOLIC LABELS                LTHT     $ABBR REPLACE
SYMBOLIC LABELS                LETA     $ABBR REPLACE
SYMBOLIC LABELS                LEPS     $ABBR REPLACE

REFERENCES: Guide I, section B.2; Guide V, Appendix 4

5 NONMEM FILE CONTROL STREAM

MEANING: NONMEM File Control Records

CONTEXT: NONMEM input file

DISCUSSION:

The NONMEM File Control Stream provides the names of optional files to be opened by NONMEM. It is read by NONMEM from a file whose name is given on the FILE record of the NONMEM Control Stream.

When NM-TRAN is used, NM-TRAN creates the NONMEM File Control Stream in a file named FSTREAM.

Each NONMEM File Control Record begins with a 4-character preface (record label) which identifies the record.

Record type Prefix Corresponding NM-TRAN record

DATA                              DATA     $DATA ...
MODEL SPECIFICATION FILE INPUT    MSFI     $MSFI ...
MODEL SPECIFICATION FILE OUTPUT   MSFO     $ESTIMATION MSFO=...
TABLE                             TABL     $TABLE FILE=...

Problem delimiter **** none

Multiple TABLE records may be present for a given problem, one for each table to be written to a new table file.

REFERENCES: Guide I, section B.3

6 NONMEM OUTPUT FILES

MEANING: NONMEM output files

CONTEXT: NONMEM output file

DISCUSSION:

NONMEM produces several output files.

First is the NONMEM report file. The name of this file is specified by the user on the nmfe command. Help entries describe the various sections of the report.

(See DATA_SET,DATA_RECORDS,DATA_ITEMS).
(See INITIAL_ESTIMATE,MONITORING_OF_SEARCH).
(See MINIMUM_VALUE_OF_OBJ._FUNCTION,FINAL_PARAMETER_ESTIMATE).
(See ETABAR,STANDARD_ERROR_OF_ESTIMATE).
(See SHRINKAGE).
(See CORRELATION_MATRIX_OF_ESTIMATE,COVARIANCE_MATRIX_OF_ESTIMATE).

With NONMEM 7, tag labels are present in the report file to allow a third-party program to find the appropriate positions in the file without having to search for specific words in the text. (a more efficient way of extracting numerical results from the analysis is from the raw and additional output files (see below)). Tag labels are:

#PARA (NM72): This tag identifies the parallelization file and number of nodes used, if parallel estimation is performed.
#TBLN (NM72): This tag specifies that following it, on the same line, will be found an integer that refers to the number of this estimation method. This number is also the table number listed in the title to tables in the various output files (raw output file, .cov, .cor, etc). The table number is incremented for each $EST statement, across all problems in the control stream file.
#METH: This tag specifies that following it, on the same line, will be found a text that describes the method, for example First Order Conditional Estimation Method with Interaction.
#TERM: This tag indicates that beginning on the next lines, text describes the termination status of the analysis.
#TERE: This tag indicates the end of the lines describing the termination status of the analysis. Thus, a software program may transfer all lines between #TERM: and #TERE: to a summary file.
#OBJT: Indicates that following it, on the same line, is the text describing the objective function, such as Minimal Value Of Objective Function.
#OBJV: Indicates that following it, on the same line, is the objective function value.
#OBJS: Indicates that following it, on the same line, is the objective function standard deviation (MCMC Bayesian analysis only).
#OBJN (NM73): Indicates that following it, on the same line, is the nonparametric objective function value.
#CPUT (NM73): Total CPU time. It is an accurate representation of the computer usage, whether single or parallel process. The same problem when run singly or in parallel will report a similar cpu time. This is in contrast with elapsed time, which is improved with parallelization.

With NONMEM 7, raw and additional output files are generated to capture parts of the report file.

The raw output file is called root.ext, or named by the FILE option of the $ESTIMATION record. (See raw_output_file).

The additional output files capture portions of the report file. (See additional_output_file). They are listed in the same order as in additional_output_fil.

root.phi root.iph (NM75) root.phm (NM72) root.shk (NM72) root.shm (NM73) root.grd (NM72) root.xml (NM72) root.cov root.clt (NM74) root.cor root.coi root.cnv (NM72) root.smt (NM72) root.rmt (NM72) root.imp (NM73) root.npd (NM73) root.npe (NM73) root.npi (NM73) root.npl (NM74) root.fgh (NM73) root.agh (NM73) root.vpd (NM74) root.ets (NM74) root.bfm (NM75) root.cpu (NM73) msfroot_ETAS msfroot_RMAT, msfroot_SMAT (NM73)

REFERENCES: Guide Introduction_7

7 RAW_OUTPUT_FILE

MEANING: NONMEM Raw Output file

CONTEXT: NONMEM Output Files

DISCUSSION:

With NONMEM 7, a NONMEM run produces several additional output files. These provide a more efficient way of way of extracting numerical results from the analysis than by obtaining them from the NONMEM report file. (See additional_output_file).

Names of the files start with “root”, where root is the root name (not including extension) of the NM-TRAN control stream file given at the nmfe7 command line, or root=“nmbayes” if the control stream file name is not passed as an argument to the NONMEM executable. E.g., in this example the root is myexample. nmfe7 myexample.ctl myexample.res The raw output file (“root.ext”) will be named myexample.ext

A different name for this file may be specified using the FILE=filename option of the $ESTIMATION record. This filename is used for all subsequent problems, until a new FILE=filename option is coded. The raw output file is only generated if the $ESTIMATION record is present and accumulates information from each Estimation step.

The first two lines of each file is the same. First is a header line that begins with the word TABLE, such as:

TABLE NO. n:

Next on the header line is the analysis text (same as given on the #METH: line in the report file), e.g., “First Order”.

In the raw output file, the analysis text is followed by the goal function text (same as given on the #OBJT: line in the report file), e.g., Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION At the end of the header line is:

Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0: Superproblem2=0 Iteration2=0

The second line of the raw output file contains the column headers for the table, all on one line.

Values of the Parameters and of the objective function are printed to the raw output file every PRINT iterations. The default order is: ITERATION THETA, SIGMA, OMEGA, OBJ (Objective function). Values of Sigma and Omega are in the original parameterization, as in the file INTER. The option ORDER of the $ESTIMATION record may be used to change the order of THETA, SIGMA, and OMEGA. (See order_option).

The iteration number, which is the first value in every line, is typically positive, but also may be negative under the following conditions:

The burn-in iterations of the MCMC Bayesian analysis are given negative values, starting at -NBURN, the number of burn-in iterations requested by the user. These are followed by positive iterations of the stationary phase.
The stochastic iterations of the SAEM analysis are given negative values. These are followed by positive iterations of the accumulation phase.
Iteration -1000000000 (negative one billion) identifies the line that contains the final result (thetas, omegas, and sigmas, and objective function) of the particular analysis. These are the value in the NONMEM output file that are labelled FINAL PARAMETER ESTIMATE. The order is theta, sigma, omega.
Iteration -1000000001 identifies the line that contains the standard errors of the final population parameters. These are the value in the NONMEM output file that are labelled STANDARD ERROR OF ESTIMATE. The order is theta, sigma, omega. This line is present if the Covariance Step is successful, or with METHOD=BAYES.
Iteration -1000000002 identifies the line that contains the eigenvalues of the correlation matrix of the variances of the final parameters.
Iteration -1000000003 identifies the line that contains the condition number , lowest, highest, Eigenvalues of the correlation matrix of the variances of the final parameters.
Iteration -1000000004 identifies the line that contains the OMEGA and SIGMA elements in standard deviation/correlation format
Iteration -1000000005 identifies the line that contains the standard errors to the OMEGA and SIGMA elements in standard deviation/correlation format
Iteration -1000000006 identifies the line that indicates 1 if parameter was fixed in estimation, 0 otherwise.
Iteration -1000000007 lists termination status (first item) followed by termination codes. In nm73, termination status catalogs the error status: For traditional analyses, an error number is listed. If negative, the analysis was user-interrupted For EM/Bayes analysis, error numbers map as follows: 0,4: optimization was completed 1,5: optimization not completed (ran out of iterations) 2,6: optimization was not tested for convergence 3,7: optimization was not tested for convergence and was user interrupted 8,12: objective function is infinite or all individual objective fuctions are zero. problem ended 16,20: All individual objective fuctions are zero. problem ended 4,5,6,7,12,20: reduced stochastic/stationary portion was not completed prior to user interrupt
Iteration -1000000008 lists the partial derivative of the likelihood (-1/2OFV) with respect to each estimated parameter. This may be useful for using tests like the Lagrange multiplier test.

See the description of root.xml in Guide INTRODUCTION TO NONMEM 7 for versions 7.4 and higher.

A file simliar to the raw output file is root.cnv. This file contains convergence information for the Monte Carlo/EM methods, if CTYPE>0:

Iteration -2000000000 identifies the line that contains the mean of last CITER values (mean objective function is that of second to last CITER values)
Iteration -2000000001 identifies the line that contains the standard deviation of last CITER values (for objective function, STD of second to last CITER values)
Iteration -2000000002 identifies the line that contains the linear regression p-value of last CITER values against iteration number. (for objective function, p-value of second to last CITER values)
Iteration -2000000003 identifies the line that contains the Alpha used to assess statistical significance (p-value<alpha)

Please note the following: The Sigma values are in their Cholesky format, as this is the form in which convergence of these values are tested. The Alpha are those based on ones actually used for convergence test of that parameter, or which would have been used on that parameter if CTYPE were of proper type. The alpha may be bonferoni corrected because of multiple comparisons, depending on number of parameters that were tested or would have been tested. Objective function alphas are not bonferoni corrected.

For importance sampling and iterative two stage, the average objective function listed in root.cnv could be used as an alternative to the final objective function for likelihood ratio tests.

REFERENCES: Guide Introduction_7