Chapter X - Other Files on the Distribution Medium
This chapter discusses the remaining files on the distribution medium.
Along with NONMEM the user will find on the distribution medium two separate programs, called here support utilities. These programs are in file 14 ("NMUTIL"), each preceded by a "CD" routine header as is usual with the other files. However, each is a separate program. The file must be separated into individual programs and each program compiled.
Oftentimes the user will initially key the control stream into a file with variable length physical records. NONMEM expects the file containing the control stream to have fixed length records of length 80. The support utility, PAD, produces the required fixed length record file from a variable length record file. This utility may also be useful when a data stream is not embedded in the control stream and ends with a FINISH record (see NONMEM Users Guide, Part II). For in this case, the file containing the data stream must also consist of fixed length records of length 80. The second support utility, PRINT, concerns the output report. The NONMEM file containing the output report can not in fact (in general) be sent to a printer. It contains the familiar FORTRAN carriage control characters: blank, 0, 1 and +, which are, however, not a part of the ANSI standard and which are not understood by ASCII printers. PRINT translates this file into one that has the appropriate ASCII carriage control characters and that can be sent to an ASCII printer.
This support utility produces an output file of records, each of length 80, from an input variable length record file. Each (logical) record of the input file is padded with the required number of blanks so that the total number of characters in the corresponding output file (logical) record contains 80 characters. The input and output files should be preconnected to FORTRAN logical units 5 and 6, respectively.
Some FORTRAN compilers have an extension that allows a sequential, variable length record file to be opened by a FORTRAN program in such a way that each record of the file is automatically padded by blanks up to a specifiable record length when the record is read by the program. If the user is working with such a compiler, then rather than use the PAD program, we suggest that this special compiler extension be used. To do this, insert an appropriate OPEN statement before the statement REWIND 5 in subroutine OFILES. For example,
OPEN (5, RECL = 80)
Alternatively, the OPEN statement can be made more elaborate so as to specify a connection between unit 5 and a physical file. However, we suggest that FORTRAN logical unit 5 be connected as described in Chapter III, Section 4.3.
This support utility produces an ASCII printer file with the appropriate ASCII control characters from a sequential file containing FORTRAN carriage control characters. The output file may be sent to an ASCII printer. The input file should be preconnected to FORTRAN logical unit 5. The output file connection is made by the program; the file name specifier for this file is PRINTOUT. The PRINT utility may be useful with the Microsoft and DIGITAL FORTRAN compilers.
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MS-DOS: |
PRINT < report-file
The output file, PRINTOUT, should be printed using a non-proportional font in landscape orientation.
Some FORTRAN compilers may have an extension that allows a sequential file to be opened by a FORTRAN program in such a way that records written to it will have appropriate ASCII carriage control characters though the program per se places FORTRAN carriage control characters into the records it writes to this file. If the user is working with such a compiler, then rather than use the PRINT program, we suggest that this special compiler extension be used. (We also, however, suggest that this extension be well checked out by the user himself, for some compilers we have seen which attempt to implement this extension have not done this successfully.) To do this, insert an appropriate OPEN statement before the statement REWIND 5 in NONMEM subroutine OFILES. For example,
OPEN (6, CARRIAGE = ’FORTRAN’)
Alternatively, the OPEN statement can be made more elaborate so as to specify a connection between unit 6 and a physical file. However, we suggest that FORTRAN logical unit 6 be connected as described in Chapter III, Section 4.3.
File "SEP" contains the source code for the FORTRAN program SEP, which is shown in Chapter III. Program SEP can be used to separate the individual routines in Files NMD, PPD1, PPD2, etc. of the distribution medium. The record length is 80 bytes. No "CD" routine header is present in this or any of the files that follow on the distribution medium.
In Chapters III, IV and V, we recommend that you try simple test cases after installing each component of the NONMEM system. The necessary files necessary for these tests are printed in other Users Guides, and are also provided on the distribution medium. In all cases, the record length is 80 bytes. These files are:
PRED1 - PRED subroutine for Chapter III (NONMEM)
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Printed as Figure 1 in NONMEM Users Guide I. |
CONTROL1 - Control file for Chapter III (NONMEM)
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Printed as Figure 2 in NONMEM Users Guide I. |
PK1 - PK subroutine for Chapter IV (PREDPP)
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Printed as Figure 7 in NONMEM Users Guide VI. |
ERROR1 - ERROR subroutine for Chapter IV (PREDPP)
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Printed as Figure 11 in NONMEM Users Guide VI. |
CONTROL2 - Control file for Chapter IV (PREDPP)
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Printed as Figure 25 in NONMEM Users Guide VI. |
CONTROL3 - Control file for Chapter V (NM-TRAN)
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Printed in Appendix IX in NONMEM Users Guide IV. |
DATA3 - Data file for Chapter V (NM-TRAN)
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Printed in Appendix IX in NONMEM Users Guide IV. |
PHENO - Phenobarbital Data
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This is the complete data for the Phenobarbital example used in NONMEM Users Guide V (Introductory), Chapters II and XI. The record length is 80 bytes. There are 745 lines in the file. |
THEO - Theophylline Data for PRED
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This is the theophylline data for the first illustrative run of Chapter I, Section 2.5 of this guide, which uses PRED abbreviated code, not PREDPP. The data are printed in Users Guide IV, Appendix II. The record length is 80 bytes. There are 132 lines in the file. |
THEOPP - Theophylline Data for PREDPP
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This is the theophylline data for the second, third, and fourth illustrative runs of Chapter I, Section 2.5, of this guide, which use PREDPP. The data are printed in NONMEM Users Guide IV, Appendix VI. The record length is 80 bytes. There are 144 lines in the file. Note that the data of THEO are identical to that of THEOPP, except that each subject’s dose amount is recorded separately from his first plasma concentration, as required with PREDPP. |
CONTROL4 - Theophylline control file: PRED abbreviated code
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This is a double precision version of the the NM-TRAN control stream for the first illustrative run of Chapter I, Section 2.5, of this guide. The contents of the file is printed in Users Guide IV, Chapter I. If you are installing single precision NONMEM, insert this record prior to the $PRED record: $SUBROUTINES SP The data of file "THEO" should be used with this control stream. |
CONTROL5 - Theophylline control file: PREDPP with ADVAN2
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This is a double precision version of the NM-TRAN control stream for the second illustrative run of Chapter I, Section 2.5. The contents of the file is printed in Users Guide IV, Chapter V. If you are installing single precision NONMEM, modify the $SUBROUTINES record as follows: $SUBROUTINES ADVAN2 SP The data of file "THEOPP" should be used with this control stream. It produces essentially the same result as the first illustrative run, but uses PREDPP and the One Compartment Model with First Order Absorption (ADVAN2). |
CONTROL6 - Theophylline control file: PREDPP with ADVAN7
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This is a double precision version of the NM-TRAN control stream for the third illustrative run of Chapter I, Section 2.5. The contents of the file is printed in Users Guide IV, Appendix VIII. If you are installing single precision NONMEM, modify the $SUBROUTINES record as follows: $SUBROUTINES ADVAN7 SP The data of file "THEOPP" should be used with this control stream. It produces essentially the same result as the second illustrative run, but uses PREDPP and the General Linear Method with Real Eigenvalues (ADVAN7). Normally, one would not use ADVAN7 when it is possible to use ADVAN2 because of the increased run time, but this is done here to provide an illustration of comparative executable sizes and run times. |
CONTROL7 - Theophylline control file: PREDPP with ADVAN6
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This is a double precision version of the NM-TRAN control stream for the fourth illustrative run of Chapter I, Section 2.5. The contents of the file is printed in Users Guide IV, Appendix VIII. If you are installing single precision NONMEM, modify the $SUBROUTINES record as follows: $SUBROUTINES ADVAN6 SP The data of file "THEOPP" should be used with this control stream. It produces essentially the same result as the second illustrative run, but uses the General NonLinear Kinetics Method (ADVAN6). Normally, one would not use ADVAN6 when it is possible to use ADVAN2 because of the increased run time, but this is done here to provide an illustration of comparative executable sizes and run times. |
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