When YADA calls your data construction file, measurement equation file, and your files with parameters to update and initialize, it copies these files into the tmp directory. The tmp directory is set to the matlab path while YADA is running. Before YADA shuts down, the files in the tmp directory are deleted and the original matlab path is restored. The advantages of this approach are mainly (i) that YADA adds as little as possible to the matlab path while it is running, and (ii) to run YADA you don't need to add any directories to your matlab path. In fact, you shouldn't add any YADA directories to your Matlab path.
However, it also means that any files that are located in, for instance, the same directory as your original data construction file will typically not be found by YADA (and by matlab). Hence, if you wish to call your own functions within, say, the data construction file you need to make sure that the directory where they are located is on the matlab path.
It is also important to keep in mind that since YADA deletes all files it finds in the tmp directory just before it shuts down, the solution to this problem is not to copy your files to the tmp directory.
Example
This example shows how you can temporarily add your own directory to the matlab path. You can, of course, add additional directories using this procedure.
function StructureForData = MyDataConstructionFile
%
% collect the original path
%
OrigPath = path;
%
% add my own directory to the path
%
path('C:\localdir',path);
%
% do a bunch of really important stuff with my data
%
.
.
.
%
% restore the original path
%
path(OrigPath);
%
% end of MyDataConstructionFile.m
%
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