# Project Archives: help and advice

Consult the reference manual and tutorials for further details and worked examples.
W.G.Bardsley, University of Manchester, U.K.

Analysing multiple data sets.

There are four ways to input multiple data sets into Simfit.

1. Sytematically copying from the clipboard or single files.
   If you ever do this you need help. This is definitely not the way to do it.
2. Using multiple selection of highlighted files with Alt and Ctrl keys.
   Much better. You must however at least investigate the Project Archive technique as such a technique requires all the files to have the same extension and exist in the same folder, whereas this is not necessarily true for Project Archives.
3. Using a library file.
   The best method. If you do it this way you obviously have arrived.
4. Using a Project Archive.
   This is a convenient way to store files with the same formatting but not necessarily the same file extension, or existing in several folders thus making multiple file selection from the usual Windows control impossible. A set of files selected from a Project Archive will be referred to as a [SELECTION].

Multiple data sets and Project Archives

Sometimes you need to supply several data files to SIMFIT, and it can be tedious to select files individually. Some examples would be as now listed.

1. Using SIMPLOT to plot many ASCII coordinate files on the same graph.
2. Using SIMSTAT for interactive ANOVA and other statistical tests requiring columns of data.
3. Using DEQSOL to fit a system of differential equations to data files for selected individual components.
4. Using QNFIT to supply starting estimates and limits in sets of parameter/limits files.
5. using QNFIT to fit multiple models with several components which require a data set for each component sub-model.

A Project Archive file is simply an ASCII text file with a list of file names, where all the files have identical formatting. You can easily create or edit such files using any text editor, however this program uses the multiple file selection control so that only existing files with correct paths and formatting are referenced. This program can be used to add files to a Project Archive or to make a [SELECTION] from such a file.

As you must restrict the file types required to build the Archive file, all files will be tested after you have made the [SELECTION], and invalid files will be de-selected, with warnings. Some examples would be:

- Vector files are used to store samples for statistical analysis. They have 1 column, like normal.tf1.
- Matrix files are used to store contingency or ANOVA data. They have several columns, like chisqd.tf4 or anova2.tf1.
- Coordinate files are used for plotting. They have 2, 3, 4 or 6 columns, like errorbar.tf1, or errorbar.tf2.
- Curve fitting files have either 2 columns (x, y) or else 3 columns (x, y, s) like polnom.tf1.
  They can also be used for plotting in program SIMPLOT.
- Encapsulated Postscript files (*.ps or *.eps) must start with %! and have a valid BoundingBox, like simfig1.ps.
- Covariance matrix files store data after model fitting.
  They are used for retrospective model discrimination.
- SVG scalable vector files (Only *.svg files created by Simfit).

If invalid files are detected, the program returns to the file [SELECTION] control so you can continue to rebuild the Project.

Types and location of Project Archives

The Project Archive listing files are stored in your

    ...ProgramData\Simfit\user\cfg

folder and are as follows:

         a_recent.cfg ... all file types
         v_recent.cfg ... vector files
         m_recent.cfg ... matrix files
         g_recent.cfg .. graphics files
         f_recent.cfg ... curve fitting files
         p_recent.cfg ... EPS (encapsulated PostScript files)
         c_recent.cfg ... parameter/covariance-matrix files
         s_recent.cfg ... SVG (scalable vector graphics files)

Of course, if you fully understand the contents of a Project Archive file, you can add files, delete files, or rearrange the order of files using a text editor such as Notepad, but Simfit provides a way to perform several editing procedures in such a way that no false files can be added to it or selected from it for convenient use, e.g. plotting selected graphics files. The way this works in Simfit is as follows.

1. If no Project Archive file exists and one is requested then a new file is opened to populate it.
2. If a Project Archive file has become overfull or needs rearranging, then open it and edit in a text editor such as Notepad.
3. If a Project Archive file is deficient in any way, such as accidently containing files that are incorrectly formatted, simply delete it and Simfit will create a new one on demand.
4. Making a [SELECTION]. Ths is simply a set of files that can be input as new files or extracted from exiting Project Archive files.
5. To add files to a Project Archive file use the control provided to add new files to a [SELECTION]. On exit from the control you will be given the option to add all new files to the corresponding Archive.
6. To extract a set of files from an Archive simply make a [SELECTION] of files from the Archive including new files if necessary. The [SELECTION] will then be passed on for the use intended and if there any new files you will be given the option to add them to the Archive if you want to.
7. Simfit checks a Project Archive when it is opened and, if any files on the list no longer exist, missing files will be removed from the list, for obvious reasons.

Summary of details about project archive file formats

The Simfit code to create, edit, or use project archives attempts to ensure that each project archive list only contains files consistent with the particulat type required. Some Simfit programs routinely offer an option to add a recently created file to the corresponding archive. For instance, graphics coordinate files saved from Simple Graphics, or parameter/covariance matrix files created by program QNFIT.
The precise format required for each type is now described.

1. a_recent.cfg ... all file types
   Arbitrary files with no restrictions.
2. v_recent.cfg ... vector files
   These files must have a title, then number of rows (NROWS) and columns (NCOLS) subject to NROWS > 0, and NCOLS = 1.
3. m_recent.cfg ... matrix files
   These files must have a title, then number of rows (NROWS) and columns (NCOLS) subject to NROWS > 0, and NCOLS > 0.
4. g_recent.cfg .. graphics files
   These files must have a title, then number of rows (NROWS) and columns (NCOLS) subject to NROWS > 0, and NCOLS = 2 (i.e., x, y), or NCOLS = 3 (i.e. x, y but weights ignored in column 3), but NCOLS not equal to 5 or 6.
5. f_recent.cfg ... curve fitting files
   These files must have a title, then number of rows (NROWS) and columns (NCOLS) subject to NROWS > 0, and NCOLS = 2 (i.e. x, y), or NCOLS = 3 (i.e. x, y, s). If NCOLS = 3 then the column of weights must be positive, but when checking only the first row is analysed for s > 0.
6. p_recent.cfg ... EPS (encapsulated PostScript files)
   The file must conform to the strict Simfit EPS format. Such files can be added to the archive each type a new Simfit EPS file is created.
7. c_recent.cfg ... parameter/covariance-matrix files
   These have a very strict format so they can be created on demand after fitting a model to data using program QNFIT, then added to the archive list. They are used to compare fits for the same models to alternative data sets.
8. Format for parameter and covariance matrix estimates

       Line 1: title
       Line 2: No. rows, no. of columns
       Line 3: cv(1,1), cv(1,2), ..., cv(1,n)
       Line 4: cv(2,1), cv(2,2), ..., cv(2,n)
       ...
       Line n + 2: cv(n,1), cv(n,2), ..., cv(n,n)
       Line n + 3: p(1), p(2), ..., p(n) estimates
       Line n + 4: NPTS = no. data points, ..., unassigned
       Line n + 5: NFREE = no. free parameters, ..., unassigned
       Line n + 6: ISTATE = 0 for fixed and 1 for free parameters

9. s_recent.cfg ... SVG (scalable vector graphics files)
   These files must conform to the strict Simfit SVG format which is a sub-set of the SVG standard.