Hi there,

Yes, indeed, if you have Category1 with D rate classes and Category2 with S rate classes, then the index for the (i,j) pair of rates [0≤i<D, 0≤j<S] is i*S + j.
To see which of the category variables is first use code like this:

Code:

GetInformation (categVarIDs,lf);
 

categVarIDs is a matrix of strings listing the ordering of category variables.

HTH,
Sergei

Hi there,

The order is consistent for all sites; you only need to call GetInformation once per likelihood function.

Sergei

Hello again Sergei,

More significantly, the following code does not seem to work:

GetInformation (categVarIDs,lf)
fprintf (stdout, categVarIDs);

Please advise.

Hi Sergei,

I would also like to know that if all the other code is different except for the category variable initialization, including the order of the initialization, will the order still be the same, so long as the variables are initialized with the same code? Ie:

Test 1:
code code code
Category1 = xyz
Category2 = abc
code code code

Test 2:
different code different code different code
Category2 = abc
Category1 = xyz
different code different code different code

My HYPHYMP Version: "/HYPHY 2.1120130515beta(MP) for Linux on x86_64\"; should I upgrade?

As for "GetInformation (categVarIDs,lf)" I literally just want my HYPHY results to have the order printed so that I can make sense of the category matrix numbers. Perhaps my "fprintf (stdout, categVarIDs);" statement is incorrect? I was under the impression that categVarIDs was an object that I could just print?

Thanks kindly,


Armen

PS. My code is as follows:

ConstructCategoryMatrix (perSiteIndex, lf, INDEX);

counter = 0;
for (k=0; k < filteredData.sites; k=k+1)
{
  fprintf (stdout, perSiteIndex[k], " ");
}

fprintf (stdout, "\n\n");

GetInformation (categVarIDs,lf)       <---I just realized there was no semicolon; will rerun with a semi-colon

/*I have tried:*/
fprintf (stdout, categVarIDs);
/*and*/
for (k=0; k < filteredData.sites; k=k+1)
{
  fprintf (stdout, categVarIDs[k], " ");
}