18 NONMEM Users Guide and On-line Help

Modern web version

A searchable web version of the NONMEM on-line help (the nmhelp material described below) is available at https://nmhelp.tingjieguo.com.

This chapter discusses documentation that can be found on the NONMEM distribution medium.

1 PDF Guides

The guides directory contains all parts of the NONMEM Users Guide as PDF files. These files may be searched and displayed on-line. They may also be printed.

Name of Documentation	Description/Title
I.pdf	Users Basic Guide
II.pdf	Users Supplemental Guide
III.pdf	NONMEM 7.6 Installation Guide
IV.pdf	NM-TRAN Guide
V.pdf	Introductory Guide
VI.pdf	PREDPP Guide
VII.pdf	Conditional Estimation Methods
VIII.pdf	Help Guide
nm760.pdf (intro7.pdf)	Introduction To Nonmem 7.6.0
Supp.pdf	NONMEM V Supplemental Guide
Intro.pdf	Introduction to Version VI
Nonmem7_technical_guide.pdf	Technical Guide on the Expectation-Maximization Population and Monte Carlo Analysis Methods in the NONMEM 7 Program
cvs_guide.pdf	Guide on CVODES (ADVAN14)
cv_guide.pdf	Guide on CVODE (ADVAN14)
idas_guide.pdf	Guide on IDAS (ADVAN15)
ida_guide.pdf	Guide on IDA (ADVAN15)

2 On-line Help

Directories help and html contain the same material that is distributed as pdf files NONMEM Users Guide Part I- Part VIII, Help Guide. In addition, they contain files that enable the material to be searched and displayed conveniently when installed on a computer. When installed as suggested, they implement the On-line Help feature of NONMEM. Their installation and use is optional.

2.1 HTML help

The HTML versions work with all web browsers such as Internet Explorer, Netscape, Firefox, etc., and can be used with all operating systems. As of NONMEM VI 2.0, the html directories contain sub-directories I, II, III, etc, containing NONMEM Users Guides I, II, III, etc. in html format. These are provided so that references between and within Users Guides can be followed by the browser as hyperlinks. This feature is not fully implemented.

Start a web browser such as Internet Explorer, Netscape, or Firefox. On the File menu, you should find a button called Open or Open File. Type (or browse for) the directory, e.g., c:or /export/home/nm760/html. Type the file name index.htm (not $index.htm). This should open a page with the title This is the main index of Hyper-NMhelp.

You may find it convenient to bookmark the page.

The use of Hyper-NMhelp is straightforward. Note that the keywords may be grouped somewhat differently than they are with the command-line on-line help described in the following sections.

2.2 COMMAND-LINE HELP (nmhelp)

Help files are intended for command-line usage, and may be useful when working from a UNIX or MS-DOS command prompt, or if there is no web browser available. Dos_tools allow convenient command-line help under MS-DOS. Users with other operating systems can use the command-line Help material, but they may have to create their own user-interface for search and display; the UNIX and MS-DOS examples may serve as convenient starting points.

The Help Guides consists of two sections: an index, which is printed in two parts (RESERVED WORDS and MISCELLANEOUS TOPICS); and over 200 individual discussions, which are also printed in two parts (DETAILED DESCRIPTIONS and EXAMPLES). In the Help directory, a file named index contains both parts of the printed index, in a format designed for use by the UNIX and DOS tools included on the distribution medium. Also on the Help Guide directory are over 200 files with names of the form xxxx.xxx, each of which contains the text of a single individual discussion. These files are referred to collectively as “detailed description files” in the examples below. (The suffix identifies the content. For example, examples have names ending with the suffix exa.)

If you opted to have the help manual installed when you ran SETUP76, then the nonmem directory (such as c:or /export/home/nm760/help) will contain the console/command line help system, nmhelp. The nmhelp file is either a DOS executable (nmhelp.exe), or a Unix bash script (nmhelp).

To use the nmhelp system in DOS, you must be in the help directory,

cd c:\nm760\help

Then select a topic, such as:

nmhelp ADVAN9

To use the nmhelp system in unix,

cd ~/nm760/help

Then select a topic, such as:

./nmhelp ADVAN9

In unix, you may execute nmhelp from any directory if you do the following. Insert the following line into your login file, such as the file .bashrc in your user directory:

alias nmhelp=~/nm760/help/nmhelp

or whatever directory your nonmem directory is located. Then, you may enter

nmhelp

from any directory.

To get information on the command nmhelp itself, enter “nmhelp help”

To get a list of the topics available, enter “nmhelp”.

To get information on a given reserved word or topic, enter “nmhelp” followed by the reserved word or topic. For example,

nmhelp nonlinear

Help for nonlinear is available in the following documents:
1 ADVAN10                 4 NONMEM model
2 ADVAN6 ADVAN8           5 NONMEM program
3 ADVAN9                  6 Michaelis Menten example

Your choices:
enter "p number" to print a document (e.g., p1 or p 1)
enter the number of the document you wish to see
enter <CR> to see document number 1
enter q <CR> to quit this list

A number 1 through 6 may be entered, and the appropriate document will be displayed at the terminal. You may then enter a different number to display a different document.

2.3 Information about the DOS Tools Components (nmhelp.exe)

nmhelp.exe: A compiled C-program that searches for and displays detailed description documents. It must be used on a 386-based DOS system or higher. It uses utility programs from the Free Software Foundation.
nmhelp.c: The source code for nmhelp, in case it is necessary to re-compile it on your system. A C or C++ compiler will be required if you choose to modify the code and create a new nmhelp.exe by running nmhelp_win.bat; we do not provide it.
gawk.exe, grep.exe: Compiled utility programs from the Free Software Foundation. Must be used on a 386-based DOS system or higher.

Other files in the Dos_tools directory are gnulic.txt (a license agreement from the Free Software Foundation which should be read by anyone who wishes to make the utilities available to others).

2.4 Using nmhelp with Ordinary MS-DOS commands

Here is a very rudimentary way to search and display the contents of the Help Guide, using ordinary DOS commands. A better way involves the use of nmhelp, described in the previous section.

Change to the directory into which you read the Help files.

To get information on a given reserved word or topic, enter “find” followed by the reserved word or topic in quotes (““). For example,

find "nonlinear" index

---------- INDEX
advan10.ppp˜ ADVAN10˜ nonlinear kinetics model
advan68.ppp˜ ADVAN6 ADVAN8˜ general nonlinear kinetics model advan68.ppp˜
ADVAN6 ADVAN8˜ nonlinear kinetics model advan9.ppp˜ ADVAN9˜ general
nonlinear kinetics model advan9.ppp˜ ADVAN9˜ nonlinear kinetics model
nonmod.gen˜ NONMEM model˜ nonmem nonlinear mixed effects model nonpro.gen˜
NONMEM program˜ nonmem nonlinear mixed effects model michaeli.exa˜ Michaelis
Menten example˜ nonlinear kinetics model

The first column lists detailed description files. The second column gives their titles. The third column gives the context in which the search word “nonlinear” appears as a keyword in these files. (The column delimiter is the character ˜).

To display a document in the list, enter “more” followed by the filename. For example,

more < advan10.ppp