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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifndef RATEGAMMAINVAR_H
#define RATEGAMMAINVAR_H
#include "rateinvar.h"
#include "rategamma.h"
/**
class for I+G rate heterogeneity
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class RateGammaInvar : public RateInvar, public RateGamma
{
public:
/**
constructor
@param ncat number of rate categories
@param tree associated phylogenetic tree
@param testAlpha turn on option for doing random restart optimization of alpha and p_invar
*/
RateGammaInvar(int ncat, double shape, bool median, double p_invar_sites, string optimize_alg, PhyloTree *tree, bool testParamDone);
/**
* check whether +I+G is used
*/
virtual bool isGammai() const {
return true;
}
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
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 (1.0-p_invar)/ncategory; }
/**
get the rate of a specified category. Default returns 1.0 since it is homogeneous model
@param category category ID from 0 to #category-1
@return the rate of the specified category
*/
virtual double getRate(int category) { return RateGamma::getRate(category); }
/**
set the proportion of invariable sites. Default: do nothing
@param pinv the proportion of invariable sites
*/
virtual void setPInvar(double pInvar);
/**
* 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();
/**
* @return model name with parameters in form of e.g. GTR{a,b,c,d,e,f}
*/
virtual string getNameParams();
/**
override function from Optimization class, used by the minimizeOneDimen() to optimize
p_invar or gamma shape parameter.
@param value value of p_invar (if cur_optimize == 1) or gamma shape (if cur_optimize == 0).
*/
virtual double computeFunction(double value);
/**
* setup the bounds for joint optimization with BFGS
*/
virtual void setBounds(double *lower_bound, double *upper_bound, bool *bound_check);
/**
optimize parameters
@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() { return RateInvar::getNDim() + RateGamma::getNDim(); }
/**
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[]);
/**
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);
/** TRUE to jointly optimize gamma shape and p_invar using BFGS, default: FALSE */
//bool joint_optimize;
virtual void setNCategory(int ncat);
/**
Compute site-specific rates. Override this for Gamma model
@param pattern_rates (OUT) pattern rates. Resizing if necesary
@return total number of categories
*/
virtual int computePatternRates(DoubleVector &pattern_rates, IntVector &pattern_cat);
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);
private:
/**
* Determine which algorithm is used to optimized p_inv and alpha
*/
string optimize_alg;
/**
current parameter to optimize. 0 if gamma shape or 1 if p_invar.
*/
int cur_optimize;
/**
* Optimize p_inv and gamma shape using the EM algorithm
*/
double optimizeWithEM(double gradient_epsilon);
/**
* Start with different initial values of p_inv
*/
double randomRestartOptimization(double gradient_epsilon);
};
#endif
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