Files
Abstract
Simfit can
accept data from the clipboard, from tables with or without row and
column labels (in tab-, comma-, semicolon-, space-delimited formats,
or as .xml, .html, .htm, .mht, .mhtml files), as well as from data files
in Simfit format.
You can transfer data tables directly from spreadsheet programs into
SIMFIT programs by selecting columns and copying to the clipboard,
and you can make correctly formatted files by pasting such clipboard
data tables into program MAKSIM. There are also Excel macros (*.XLS)
provided with the SIMFIT package to
enable you to create correctly formatted files from Microsoft
Office, but SIMFIT also has a suite of editors to facilitate
the creation and editing of data files. For instance,
program MAKFIL has many special features to help you create
correctly formatted data files for curve fitting, but program MAKMAT
should be used to generate data files for statistical analysis.
Program SIMPLOT can be used to make graphics files while program
MAKLIB is used to collect the names of groups of files together
into a library file for simultaneous plotting or statistical analysis.
Program MAKSIM takes in data in tabular form as an ASCII text file or
from clipboard data copied from a spreadsheet in order to select
rows and columns then generate a data file in the SIMFIT format.
SIMFIT data files can be viewed in the
SIMFIT viewer or using any text editor, e.g. NOTEPAD.
Details
It is a very bad policy to type data into programs for direct
analysis since you will almost always want to save the data to
edit or re-use. For this reason, always make data files.
You can make these by typing your data values directly into the
appropriate program or by copying from your spreadsheet program
to the clipboard and pasting into a program (MAKSIM) to generate
correctly formatted data files. All SIMFIT programs will allow
you to paste in data directly from the clipboard but this is
not recommended.
SIMFIT data files are ASCII text files that
have a very simple format, which will easily be appreciated if you
browse any test file *.tf? (e.g. MMFIT.TF1) in the viewer.
All the values in SIMFIT data files must be numerical, but any
format can be used, e.g. 100, 100.0, 1.0E2, 1.0E+02, and the
columns of numbers can be separated by tabs, semicolons (or spaces, or commas
as long as commas are not used for decimal points). Any
files not consistent with this format will be rejected with an
error message telling you what is wrong.
SIMFIT data files contain the numerical data required for curve
fitting, statistical analysis or plotting, but obviously data
must be formatted correctly. For example differential equations
are solved sequentially, so the x-values must be in increasing
order. Again, weights for fitting must be sensible positive
values, and such restrictions are built into SIMFIT editors.
The format for SIMFIT data files
Title (i.e. identifier for the data)
m n (i.e. no. rows no. columns in the data set)
... data (i.e. the m by n matrix)
... data
... data
k (i.e. the no. of further text lines)
... text (i.e. extra lines of text)
You can use any editor to make such files but you are likely
to make mistakes and produce a file that is read incorrectly
or not at all. For this reason you should always use the
SIMFIT editors to prepare or edit your data files.
Copying data from SIMFIT to the clipboard
At various points in SIMFIT you will be able to use the editor
in view-only mode. For example after doing statistical analysis
or curve fitting, or by selecting the View Text option. If you
select text when in this mode it can be copied to the clipboard
in the usual way. This is most useful when selecting a part of
a data set or a section from a results file to include in a
document. Also note that tables of data copied from the SIMFIT
viewer can be pasted into other applications.
Copying graphs from SIMFIT to the clipboard
Each time SIMFIT displays a graph there is a Copy button which
allows you to copy the current graph to the clipboard.
However you should note that all that is copied is a bitmap of
the display which, being essentially a .bmp file, will be large
and of poor resolution. This is not the best way to use SIMFIT
graphics, even though it may be convenient. The best way is to
save the graph in the .eps format since such vector files are
very small and of much higher quality. You can easily print the
.eps file or transform it into a graphics file using the built-in
options to transform *.eps files using the GhostScript dll distributed
with SIMFIT.
Copying numerical data from the clipboard into SIMFIT
Each time SIMFIT requests you to input data for analysis it
looks to see what sort of data are on the clipboard. If there
are ASCII text data, then the Paste button will become activated and
you can paste data into a temporary file for analysis. If the
first clipboard data line is numerical, SIMFIT will attempt to
generate a data file with a header and trailer, just like any
normal SIMFIT data file. For instance, if you paste two columns
from your spreadsheet onto the clipboard you will then be able
to plot them or fit them. If the result is interesting you can
save the temporary file f$??????.tmp with a chosen file name, since
SIMFIT ignores and (usually) deletes such temporary data files.
Note that to do this you paste selected columns of numerical
data with no labels. This is the rule: if there only numbers
on the first clipboard line, SIMFIT will try to create a data file.
Pasting arbitrary data from the clipboard into SIMFIT
You can leave all labels and character data in the table if you
want to use MAKSIM for data extraction, but note that MAKSIM
regards spaces as separators, so use labels like Mr_John_Smith, etc.
Advice about creating SIMFIT data files
- Use an informative title with the date of the experiment.
- The first additional text line after the end of the data
controls some programs, e.g. CALCURVE
in expert mode, but most programs ignore the text. This is
where you enter details of your experiment for posterity.
However, the use of several advanced programs is greatly
facilitated by provided by the trailer section.
For instance, starting estimates for constrained curve
fitting by program QNFIT using the expert mode.
- When using MAKFIL for curve fitting, enter all the data so
the run and sign tests have maximum power and the correct
number of degrees of freedom are used in the statistics.
If you do not have sample variances from replicates, try
an appropriate multiple of the measured response (7%?) as
a standard deviation estimate. Nothing is saved by using
means and standard errors of means. If you do input these then the
parameter estimates will be alright, but the resulting statistics will
be biased due to using the wrong number of degrees of
freedom. This will not matter in a calibration curve.
- If you enter a vector into MAKMAT, do not use the option to
rearrange into increasing or decreasing order if you wish
to do run or paired t tests which depend on natural ordering.
- With big data sets you could first make small files with MAKFIL
or MAKMAT but then join them together using EDITFL or EDITMT.
Alternatively use a spreadsheet program such as Excel with the
simfit6.xls macro.
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