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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 RATEINVAR_H
#define RATEINVAR_H
#include "tree/phylotree.h"
#include "rateheterogeneity.h"
const double MIN_PINVAR = 1e-6;
const double TOL_PINVAR = 1e-6;
/**
class for rate heterogeneity with a fraction of invariable sites
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class RateInvar : virtual public RateHeterogeneity
{
friend class RateGammaInvar;
public:
/**
constructor
@param p_invar_sites proportion of invariable sites
@param tree associated phylogenetic tree
*/
RateInvar(double p_invar_sites, PhyloTree *tree);
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
* @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 1.0 - p_invar; }
/**
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 1.0 / (1.0 - p_invar); }
/**
get the proportion of invariable sites
@return the proportion of invariable sites
*/
virtual double getPInvar() { return p_invar; }
/**
* 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);
/**
override function from Optimization class, used by the minimizeOneDimen() to optimize
p_invar parameter
*/
virtual double computeFunction(double p_invar_value);
/**
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[]);
/**
return the number of dimensions
*/
virtual int getNDim() { return !fix_p_invar; }
/**
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);
virtual bool isFixPInvar() const {
return fix_p_invar;
}
void setFixPInvar(bool fixPInvar) {
fix_p_invar = fixPInvar;
}
/**
set the proportion of invariable sites. Default: do nothing
@param pinv the proportion of invariable sites
*/
virtual void setPInvar(double pInvar) {
p_invar = pInvar;
}
/**
Set whether or not to optimize p_invar
@param opt TRUE to optimize p_invar, FALSE otherwise
*/
// virtual void setOptimizePInvar(bool opt) { optimize_p_invar = opt; }
/**
proportion of invariable sites
*/
double p_invar;
/**
TRUE to fix the proportion of invariable sites
*/
bool fix_p_invar;
/**
TRUE to optimize p_invar (if not fixed), FALSE otherwise (e.g. in case of mixture model)
*/
// bool optimize_p_invar;
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);
};
#endif
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