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/*
* phylotesting.h
*
* Created on: Aug 23, 2013
* Author: minh
*/
#ifndef PHYLOTESTING_H_
#define PHYLOTESTING_H_
#include "tools.h"
class PhyloTree;
class IQTree;
struct ModelInfo {
string set_name; // subset name
string name; // model name
double logl; // tree log likelihood
int df; // #parameters
double tree_len; // tree length, added 2015-06-24 for rcluster algorithm
string tree; // added 2015-04-28: tree string
double AIC_score, AICc_score, BIC_score; // scores
double AIC_weight, AICc_weight, BIC_weight; // weights
bool AIC_conf, AICc_conf, BIC_conf; // in confidence set?
};
struct TreeInfo {
double logl; // log likelihood
double se; // standard error of deltaL (logl difference to max), or square root of variance
double rell_bp; // bootstrap proportion by RELL method
bool rell_confident; // confidence set for RELL-BP
double sh_pvalue; // p-value by Shimodaira-Hasegawa test
double wsh_pvalue; // p-value by weighted Shimodaira-Hasegawa test
double kh_pvalue; // p-value by Kishino-Hasegawa test
double wkh_pvalue; // p-value by weighted Kishino-Hasegawa test
double elw_value; // ELW - expected likelihood weights test
bool elw_confident; // to represent confidence set of ELW test
double au_pvalue; // p-value by approximately unbiased (AU) test
};
/**
* computing AIC, AICc, and BIC scores
*/
void computeInformationScores(double tree_lh, int df, int ssize, double &AIC, double &AICc, double &BIC);
/**
* check if the model file contains correct information
* @param model_file model file names
* @param model_name (OUT) vector of model names
* @param lh_scores (OUT) vector of tree log-likelihoods
* @param df_vec (OUT) vector of degrees of freedom (or K)
* @return TRUE if success, FALSE failed.
*/
bool checkModelFile(string model_file, bool is_partitioned, vector<ModelInfo> &infos);
/**
testing the best-fit model
return in params.freq_type and params.rate_type
@param set_name for partitioned analysis
@param in_tree phylogenetic tree
@param model_info (IN/OUT) information for all models considered
@param set_name for partition model selection
@param print_mem_usage true to print RAM memory used (default: false)
@return name of best-fit-model
*/
string testModel(Params ¶ms, PhyloTree* in_tree, vector<ModelInfo> &model_info, ostream &fmodel,
ModelsBlock *models_block, int num_threads, string set_name = "", bool print_mem_usage = false);
/**
* print site log likelihoods to a fileExists
* @param filename output file name
* @param tree phylogenetic tree
* @param ptn_lh pattern log-likelihoods, will be computed if NULL
* @param append TRUE to append to existing file, FALSE otherwise
* @param linename name of the line, default "Site_Lh" if NULL
*/
void printSiteLh(const char*filename, PhyloTree *tree, double *ptn_lh = NULL,
bool append = false, const char *linename = NULL);
/**
* print partition log likelihoods to a file
* @param filename output file name
* @param tree phylogenetic tree
* @param ptn_lh pattern log-likelihoods, will be computed if NULL
* @param append TRUE to append to existing file, FALSE otherwise
* @param linename name of the line, default "Site_Lh" if NULL
*/
void printPartitionLh(const char*filename, PhyloTree *tree, double *ptn_lh = NULL,
bool append = false, const char *linename = NULL);
/**
* print site log likelihoods per category to a file
* @param filename output file name
* @param tree phylogenetic tree
*/
void printSiteLhCategory(const char*filename, PhyloTree *tree, SiteLoglType wsl);
/**
* print site posterior probabilities per rate/mixture category to a file
* @param filename output file name
* @param tree phylogenetic tree
*/
void printSiteProbCategory(const char*filename, PhyloTree *tree, SiteLoglType wsl);
/**
* print site state frequency vectors (for Huaichun)
* @param filename output file name
* @param tree phylogenetic tree
*/
void printSiteStateFreq(const char*filename, PhyloTree *tree, double *state_freqs = NULL);
/**
print ancestral sequences
@param filename output file name
@param tree phylogenetic tree
@param ast either AST_MARGINAL or AST_JOINT
*/
void printAncestralSequences(const char*filename, PhyloTree *tree, AncestralSeqType ast);
/**
* Evaluate user-trees with possibility of tree topology tests
* @param params program parameters
* @param tree current tree
* @param info (OUT) output information
* @param distinct_ids IDs of distinct trees
*/
void evaluateTrees(Params ¶ms, IQTree *tree, vector<TreeInfo> &info, IntVector &distinct_ids);
void evaluateTrees(Params ¶ms, IQTree *tree);
/**
get sequence type for a model name
@param model_name model name string
@param seq_type (OUT) sequence type, SEQ_UNKNOWN if is not determined
@return 1 for parametric model, 2 for empirical model
*/
int getSeqType(const char *model_name, SeqType &seq_type);
string getSeqType(string model_name);
#endif /* PHYLOTESTING_H_ */
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