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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 PARTITIONMODEL_H
#define PARTITIONMODEL_H
#include "tree/phylosupertree.h"
#include "modelfactory.h"
/**
Partition model
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class PartitionModel : public ModelFactory
{
public:
PartitionModel();
/**
constructor
create partition model with possible rate heterogeneity. Create proper class objects
for two variables: model and site_rate. It takes the following field of params into account:
model_name, num_rate_cats, freq_type, store_trans_matrix
@param params program parameters
@param tree associated phylogenetic super-tree
*/
PartitionModel(Params ¶ms, PhyloSuperTree *tree, ModelsBlock *models_block);
~PartitionModel();
/**
set checkpoint object
@param checkpoint
*/
virtual void setCheckpoint(Checkpoint *checkpoint);
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
* @param brlen_type either BRLEN_OPTIMIZE, BRLEN_FIX or BRLEN_SCALE
* @return #parameters of the model + # branches
*/
virtual int getNParameters(int brlen_type);
/**
optimize model parameters and tree branch lengths
NOTE 2016-08-20: refactor the semantic of fixed_len
@param fixed_len 0: optimize branch lengths, 1: fix branch lengths, 2: scale branch lengths
@param write_info TRUE to write model parameters every optimization step, FALSE to only print at the end
@param logl_epsilon log-likelihood epsilon to stop
@param gradient_epsilon gradient (derivative) epsilon to stop
@return the best likelihood
*/
virtual double optimizeParameters(int fixed_len = BRLEN_OPTIMIZE, bool write_info = true,
double logl_epsilon = 0.1, double gradient_epsilon = 0.0001);
/**
* optimize model parameters and tree branch lengths for the +I+G model
* using restart strategy.
* @param fixed_len TRUE to fix branch lengths, default is false
* @return the best likelihood
*/
virtual double optimizeParametersGammaInvar(int fixed_len = BRLEN_OPTIMIZE, bool write_info = true, double logl_epsilon = 0.1, double gradient_epsilon = 0.0001);
/**
* @return TRUE if parameters are at the boundary that may cause numerical unstability
*/
virtual bool isUnstableParameters();
/** optimize linked alpha parameter of over all partitions with Gamma rate */
double optimizeLinkedAlpha(bool write_info, double gradient_epsilon);
/**
override function from Optimization class, used by the minimizeOneDimen() to optimize
gamma shape parameter
*/
virtual double computeFunction(double shape);
protected:
/** linked Gamma shape alpha between partitions */
double linked_alpha;
};
#endif
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