Summary
Readme.txt for Simfit Version 7
Simfit Version 7 (for MS Windows, Mac, and Linux)
CONTENTS : 1) General Information
2) Configuration
3) Upgrading
4) Help and advice
1) General Information
======================
Summary: Simfit is a free software Open Source package for
simulation, curve fitting, statistical analysis and
graph plotting. There are now two versions.
i) The free standing Academic version does not use
the NAG library for numerical analysis, but it
does use some very reliable and robust public
domain numerical analysis code (e.g., blas, linpack,
lapack, minpack, dvode, lbfgsb, quadpack, slatec,
Applied Statistics algorithms, and ACMTOMS).
ii) The NAG library version has extra features, but it
can only be used by those who already have the NAG
library DLLs Mark >= 20 installed on their PC.
Users: Simfit is free for teaching and research purposes from
the web site at http://www.simfit.org.uk, but it
must not be sold on, or used for profit. The Spanish
version can be obtained from http://simfit.usal.es
Versions: The mainframe and PC versions up to version 5.7 are no
longer supported. Version 7 for Windows, Mac, and Linux
is the only version that is currently being supported
and developed. No email help will be given for any
versions except for version 7. To avoid confusion with
some previous versions of Simfit, version 7 files
files all have a w_ prefix, e.g., w_simfit.exe in the
32-bit version, but a x64_ prefix, e.g. x64_simfit.exe
in the 64-bit version. The file version7.txt has details.
Install: Get the self extracting setup executable file, available
in a zip file from http://www.simfit.org.uk, and double
click from Explorer. Windows users who want PostScript
options for superior quality graphics should also install
the GSview/Ghostscript package, and should have the
Adobe Acrobat Reader. Linux users have such utilities
built-in. The file install.txt has details.
Problems: The only known problem is when users have inconsistent
binaries, for which the remedy is to remove/re-install.
The file errors.txt has details.
Running: Make a desk-top shortcut to the Simfit driver w_simfit.exe
(or x64_simfit.exe). This is a special program-manager type
file designed to make it easy for you to use Simfit as
if all of the forty odd separate independent programs
were just one big program. Of course you can run any of
the individual programs from the command line, or by
executing from Explorer.
Testing: There are test data files *.tf? to use for each program
and the reference manual has worked examples showing
you how to use these.
Files: There are special editors to prepare data files, results
are always saved to file, and the package is configured by
.cfg files. Formats are described in the w_readme.f? files.
Clipboard tables can be pasted into Simfit, or used by
program Maksim to create correctly formatted data files.
Graphs: Image files are Postscript (eps, for top quality), and
also pdf, svg, png, emf, pcx, tif, jpg, or bmp.
Plots can be transformed interactively in the usual ways,
and a facility exists to transfer data interactively from
any default graphs into the advanced plotting routines.
Simfit graphics are described in the w_readme.g? files.
Interface:To transfer data from Excel into Simfit, write out tables
of data to CSV (ASCII comma-delimited files), XML, or HTML,
export files. These can be imported directly into Simfit or
read into the program Maksim. Otherwise use the clipboard.
Alternatively, use one of the special macros, like simfit4.xls
or simfit6.xls, to make correctly formatted files from Excel.
Enhanced metafiles (emf) or png files can be used to import
graphs into those programs (e.g. Word) that do not support
PostScript. To strip margins, re-size, rotate, make collages,
etc., from Simfit eps files, use program Editps.
Manuals: There is a reference manual in PS (monochrome), pdf
(colour with hyperlinks), pdf (monochrome, and LaTeX source
together with a set of PS files. If you want to see how to
create a document, like the Simfit user manuals including
figures, hyperlinks etc., use LaTeX with the *.tex, .wgb,
and *.eps files distributed from the website.
Help: There is a help program, but every program has a built in
tutorial. Please read these before running any program.
Fitting: Most of the models used in data analysis can be fitted by
dedicated routines. In addition, there are programs that
use a library of models to fit differential equations, or
one or more functions of one or several independent variables.
Users can supply models as dynamic link libraries, or in
the form of special ASCII text files (see w_readme.f4).
Stats: All the usual statistical tests are supported.
Code: The file source.txt has details.
2. Configuration
================
Simfit is configured by a set of temporary files with extension
.cfg as in w_ps.cfg, w_simfit.cfg, etc. These are all edited as
you use Simfit but, if you want to fix a particular default, you
can use archived versions to overwrite the defaults.
Typical uses for .cfg files would be storing paths to program
files, saving file search patterns, altering the colour palette,
archiving graph titles and graphical objects. If you learn how to
manipulate the .cfg files you can customise Simfit to your own
requirements. Simfit does not use the Windows registry.
3: Upgrading
============
Each release of Simfit has internal identifiers to make sure that
the executables and dynamic link libraries are self-consistent.
If you forget to upgrade w_simfit.exe or salflibc.dll, for
instance, you will get error messages. When you upgrade, make sure
you uninstall previous editions, or overwrite all executables and
dlls by upgraded versions.
4. Help and advice for Simfit users
===================================
What can Simfit do ?
====================
The Simfit package can do most simulations, statistics, curve fits
and graph plots needed in data analysis. Inevitably there will
always be things you want to do that can't be done, but it has been
designed for versatility so, to get the most from it, there are
some things you have to bear in mind.
What assumptions are made about typical users ?
===============================================
I have assumed a much higher degree of scientific competence and
computer literacy than is assumed by commercial packages. Thus, I
presumed the user would know that 1.234E+3 is 1234, and I assumed
users would know the difference between a binary and an ASCII text
file. Any user who wants to get to grips with Simfit should learn
how to browse the readme.? files, test files *.tf? and PostScript
.PS files. Furthermore, I have assumed that users will know
how to make subfolders, name files sensibly, and use some sort
of systematic naming convention to facilitate file access.
Simfit does not use or add any reserved filename extensions.
What sort of error messages does Simfit give ?
==============================================
I have not told you when to use particular mathematical models but
have assumed you would know when to choose between Mmfit, Hlfit or
Sffitt in order to fit your binding data. If this is asking too much
then perhaps you should not be using a curve fitting approach as a
black box procedure. Nonlinear regression is a very difficult area
which needs great caution to avoid over-interpetation such as, for
instance, claiming that three exponentials fit better than two. If
you ignore the advice that Simfit pours out, and long for a silent
package that just gives you the answer, just bear in mind that if
Simfit warns you about anything, the other packages should too, as
they all face the same computational problems. Error messages from
Simfit are all put there to help you avoid mistakes, and guide you
into making sensible decisions. If you ignore them, please be aware
that they were put there as the result of much experience.
Why are there so many files and programs in Simfit ?
====================================================
You may be infuriated by the large number of separate programs in
Simfit and the seemingly endless number of data and graphics files
and wonder why you can't save a complete graph as a single file. Of
course you can. You can make a PostScript file. This can be saved
as a metafile, printed out, incorporated into a document, viewed
on the screen, transformed into other formats, etc. What you cannot
do is recompose a saved PS graph with several data sets, or perhaps
error bars, with one or more best-fit curves from alternative fits
and different symbols and line types, since it is too complicated
to re-interpret graphics files in this way. On the other hand, as
long as you keep track of the appropriate ASCII text files you can
easily create the composite graph using Simplot then Editps. Again
you might wonder why you have to supply all your data for fitting
instead of just mean-y's and standard-deviations. After all, most
people plot means with error bars, not the whole data set. There is
a very good reason for this. If every design point has exactly the
same number of replicates, and this information is made available
to the fitting program, then there are fewer points to fit and the
standard errors, and other statistics, can be calculated using the
correct number of degrees of freedom. This is impossible when the
design points do not have equal numbers of replicates. In any case,
users should always inspect the best-fit and residuals plots using
all replicates.
How should I make data files ?
==============================
This is my recommendation when making data files. Always fit the
total data set, never means of replicates. Simfit is designed to
do this, and it never has to re-calculate the deterministic model
more than once at any given x-design point, since it uses logical
variables and look-up to avoid this. This is particularly valuable
with programs like deqsol which fit sets of differential equations.
To make sure starting estimates are calculated accurately and data
are plotted correctly, curve fitting data files must be in order
of increasing independent variable, i.e. x or t.
What editors are provided with Simfit ?
=======================================
Again you might wonder why you should use Editfl or Editmt, rather
than a normal text editor. By all means use a full screen editor
to change the odd data point: I do. The full power of the Simfit
editors will only become evident when you learn how easy it is to
join up files, change data weighting, calculate error bars and means
for plotting, put data into order, check data sets for consistency
before fitting, transform coordinate systems, e.g. from seconds to
minutes and so on. The Simfit editor can be used in cell mode or
line mode and can be used as a viewer with the editing functions
disabled to prevent you from altering a file format. If you want
to browse any test file, data file, results file, etc., then use
the Simfit editor in view-only mode from the menu in the program
manager w_simfit.exe. To print a Simfit results file or any text
file use the Edit/Save/Print function from the file view controls.
What graphical functions does Simfit have ?
===========================================
Graphics causes an endless source of problems. It is trivial to get
any particular plot on screen, or to transfer it to a printer. The
real problem is to save graphs, make collages, add insets, change
titles, incorporate into documents, send by email, etc. The trouble
arises since bit-maps are easy to manipulate on screen but are too
large to store, and yield poor resolution when expanded. A vector
format is best for scientific graphs, which narrows the choice to
eps, svg, or emf, or possibly compressed bitmaps such as png, but
definitely excludes .jpg, tif, .pcx, and especially bmp.
How can I get Simfit graphs into documents ?
============================================
Windows users with no PostScript facilities can create enhanced
metafiles (.emf) or portable network graphics file (.png), as these
are compact with fairly good resolution, and can be imported into
all Windows programs.
PostScript users will be able to use LaTeX/Dvips and import eps
files directly to get the highest possible quality.
The best way to get the most out of the Simfit graphics is to
save the appropriate ASCII text graphic files with data and
best fit curves as library files, or in your graphics project
archive, then read them into Simplot and make PostScript files.
Edit these for re-sizing, rotating, making collages or insets etc.
using Editps. If you don't use LaTeX/Dvips, you will be faced with
the problem of getting hardcopy from the final PostScript file, or
incorporating it into a document. If you want to view the file on
a PC screen, send it to a non-Postscript printer, transform it into
another form, e.g. a bit map, etc. then use GSview/Ghostscript.
If you don't have PostScript printing, or use a word processor that
doesn't support PostScript, make PS files then use GSview/Ghostscript
to drive your printer or transform the files into acceptable format.
to use. Most modern word-processing packages will accept Simfit
PS files directly, if they are configured correctly, since they are
consistent with the EPS convention. GSview/Ghostscript can be used
to add a preview if you insist on seeing included graphics on screen
What documentation is supplied with Simfit ?
============================================
1) The manual is in three versions as follows:
a) w_manual.ps : monochrome PS version
b) w_manual.pdf: coloured PDF version with hyperlinks
c) mono_manual.pdf: monochrome pdf version
2) Every individual program starts with a brief tutorial and
there is a set of test data files which can be as examples
for your own data or for practise. The first time you use a
Simfit program you should run it with the test files provided.
This is easy since each program is linked to specially
selected example data files.
3) There is a set of w_readme.* files covering technical details,
but these mostly datae from an earlier era and do tend to use a
fair bit of computer-speak.
4) The file ms_office.pdf covers all aspects of the integration of
Simfit with MS Office and OpenOffice.