new model
added new code for managing epsilon parameter when loading DEs
adding parameter to zagros to control epsilon
fixed nasty bug in netwon raphson, and improved speed for geo_p optimisation
moving estimation of delta in max_de func
cleaning up delta optim. code
fixed minor bug in estimation of delta; removed some old code that isn't used anymore
refactored delta optim. code a bit
Fixed a bug where the maximization_de was being called in sequence only mode
adding constant to weight total contribution of DE component to LL; fixed a couple of potential bugs
fractional pseudocount for des
changes to the scaling of DE counts
fixed bug in calc. de log like for delta estimation
added new options to allow delta and geometric p to be specified, rather than optimised, if desired. Implemented scaling of indicators to fix problem with ZOOPS when prior is too strong, changed pseudo-count back to 1 DE
fixed mistake in setting value for geo_p parameter; changed normalising constant for DE contribution to depend on expectation without DEs
Changed the default setting to optimize the delta by default and keep constant with the desired value if wanted, optimize g if desired and kept constant to a pre-determined value by default, number of starting points to 1, number of output motifs to 10
changed the default value of geo_p to the mode of the distribution when we learn g, changed the default value of number of starting points and reported motifs, and cleaned up the code
Fixed a bug where normalization was not occuring with the right values
By pre-computing the value of prior probability of motif occurance in the sequences, for fixed i,j and delta, reduced the cubic time complexity of the algorithm ine each iteration of EM to quadratic
Finalized the final set of default parameters