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/*
* ratefree.h
*
* Created on: Nov 3, 2014
* Author: minh
*/
#ifndef RATEFREE_H_
#define RATEFREE_H_
#include "rategamma.h"
class RateFree: public RateGamma {
public:
/**
constructor
@param ncat number of rate categories
@param tree associated phylogenetic tree
@param opt_alg optimization algorithm (1-BFGS, 2-BFGS, EM)
*/
RateFree(int ncat, double start_alpha, string params, bool sorted_rates, string opt_alg, PhyloTree *tree);
virtual ~RateFree();
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
@return true if this is a Gamma model (default: false)
*/
virtual int isGammaRate() { return 0; }
/**
* @return model name with parameters in form of e.g. GTR{a,b,c,d,e,f}
*/
virtual string getNameParams();
/**
get the proportion of sites under a specified category.
@param category category ID from 0 to #category-1
@return the proportion of the specified category
*/
virtual double getProp(int category) { return prop[category]; }
/**
the target function which needs to be optimized
@param x the input vector x
@return the function value at x
*/
virtual double targetFunk(double x[]);
/**
* setup the bounds for joint optimization with BFGS
*/
virtual void setBounds(double *lower_bound, double *upper_bound, bool *bound_check);
/**
optimize parameters. Default is to optimize gamma shape
@return the best likelihood
*/
virtual double optimizeParameters(double gradient_epsilon);
/**
optimize rate parameters using EM algorithm
@return log-likelihood of optimized parameters
*/
double optimizeWithEM();
/**
return the number of dimensions
*/
virtual int getNDim();
/**
write information
@param out output stream
*/
virtual void writeInfo(ostream &out);
/**
write parameters, used with modeltest
@param out output stream
*/
virtual void writeParameters(ostream &out);
/**
set number of rate categories
@param ncat #categories
*/
virtual void setNCategory(int ncat);
/**
initialize from checkpoint rates and prop from rate model with #category-1
*/
virtual void initFromCatMinusOne();
/**
* used to normal branch lengths if mean rate is not equal to 1 (e.g. FreeRate model)
* @return mean rate, default = 1
*/
virtual double meanRates();
/**
* rescale rates s.t. mean rate is equal to 1, useful for FreeRate model
* @return rescaling factor
*/
virtual double rescaleRates();
protected:
/**
this function is served for the multi-dimension optimization. It should pack the model parameters
into a vector that is index from 1 (NOTE: not from 0)
@param variables (OUT) vector of variables, indexed from 1
*/
virtual void setVariables(double *variables);
/**
this function is served for the multi-dimension optimization. It should assign the model parameters
from a vector of variables that is index from 1 (NOTE: not from 0)
@param variables vector of variables, indexed from 1
@return TRUE if parameters are changed, FALSE otherwise (2015-10-20)
*/
virtual bool getVariables(double *variables);
/**
* proportion of sites for each rate categories
*/
double *prop;
/** 1 to fix weights, 2 to fix both weights and rates */
int fix_params;
/** true to sort rate in increasing order, false otherwise */
bool sorted_rates;
/** 0: no, 1: rates, 2: weights */
int optimizing_params;
string optimize_alg;
};
#endif /* RATEFREE_H_ */
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