Counters for phylogenetic modeling. More...

Collaboration diagram for Phylo counters:

Modules
	Phylo rules
	Rules for phylogenetic modeling.

void	counter_overall_gains (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Overall functional gains. More...

void	counter_gains (PhyloCounters *counters, std::vector< size_t > nfun, size_t duplication=Geese::etype_default)
	Functional gains for a specific function (`nfun`). More...

void	counter_gains_k_offspring (PhyloCounters *counters, std::vector< size_t > nfun, size_t k=1u, size_t duplication=Geese::etype_default)
	k genes gain function nfun More...

void	counter_genes_changing (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Keeps track of how many genes are changing (either 0, 1, or 2 if dealing with regular trees.) More...

void	counter_preserve_pseudogene (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Keeps track of how many pairs of genes preserve pseudostate. More...

void	counter_prop_genes_changing (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Keeps track of how many genes are changing (either 0, 1, or 2 if dealing with regular trees.) More...

void	counter_overall_loss (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Overall functional loss. More...

void	counter_maxfuns (PhyloCounters *counters, size_t lb, size_t ub, size_t duplication=Geese::etype_default)
	Cap the number of functions per gene. More...

void	counter_loss (PhyloCounters *counters, std::vector< size_t > nfun, size_t duplication=Geese::etype_default)
	Total count of losses for an specific function. More...

void	counter_overall_changes (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Total number of changes. Use this statistic to account for "preservation". More...

void	counter_subfun (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Total count of Sub-functionalization events. More...

void	counter_cogain (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Co-evolution (joint gain or loss) More...

void	counter_longest (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Longest branch mutates (either by gain or by loss) More...

void	counter_neofun (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Total number of neofunctionalization events. More...

void	counter_pairwise_neofun_singlefun (PhyloCounters *counters, size_t nfunA, size_t duplication=Geese::etype_default)
	Total number of neofunctionalization events sum_u sum_{w < u} [x(u,a)(1 - x(w,a)) + (1 - x(u,a)) x(w,a)] change stat: delta{x(u,a): 0->1} = 1 - 2 * x(w,a) More...

void	counter_neofun_a2b (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Total number of neofunctionalization events. More...

void	counter_co_opt (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Function co-opting. More...

void	counter_k_genes_changing (PhyloCounters *counters, size_t k, size_t duplication=Geese::etype_default)
	Indicator function. Equals to one if \(k\) genes changed and zero otherwise. More...

void	counter_less_than_p_prop_genes_changing (PhyloCounters *counters, double p, size_t duplication=Geese::etype_default)
	Indicator function. Equals to one if \(k\) genes changed and zero otherwise. More...

void	counter_gains_from_0 (PhyloCounters *counters, std::vector< size_t > nfun, size_t duplication=Geese::etype_default)
	Used when all the functions are in 0 (like the root node prob.) More...

void	counter_overall_gains_from_0 (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Used when all the functions are in 0 (like the root node prob.) More...

void	counter_pairwise_overall_change (PhyloCounters *counters, size_t duplication=Geese::etype_default)
	Used when all the functions are in 0 (like the root node prob.) More...

void	counter_pairwise_preserving (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Used when all the functions are in 0 (like the root node prob.) More...

void	counter_pairwise_first_gain (PhyloCounters *counters, size_t nfunA, size_t nfunB, size_t duplication=Geese::etype_default)
	Used when all the functions are in 0 (like the root node prob.) More...

Detailed Description

Counters for phylogenetic modeling.

Parameters

counters A pointer to a PhyloCounters object (Counters<PhyloArray, PhyloCounterData>).

Function Documentation

◆ counter_co_opt()

void counter_co_opt	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Function co-opting.

Function co-opting of functions A and B happens when, for example, function B is gained as a new featured leveraging what function A already does; without losing function A. The sufficient statistic is defined as follows:

\[ x_{pa}(1 - x_{pb})\sum_{i<j}\left[x_{ia}^p(1 - x_{ib}^p)x_{ja}^px_{jb}^p + x_{ja}^p(1 - x_{jb}^p)x_{ia}^px_{ib}^p\right] \]

This algorithm implements the change statistic.

Definition at line 1299 of file counters.hpp.

◆ counter_cogain()

void counter_cogain	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Co-evolution (joint gain or loss)

Needs to specify pairs of functions (nfunA, nfunB).

Definition at line 794 of file counters.hpp.

◆ counter_gains()

void counter_gains	(	PhyloCounters *	counters,
		std::vector< size_t >	nfun,
		size_t	duplication = `Geese::etype_default`
	)

inline

Functional gains for a specific function (nfun).

Definition at line 99 of file counters.hpp.

◆ counter_gains_from_0()

void counter_gains_from_0	(	PhyloCounters *	counters,
		std::vector< size_t >	nfun,
		size_t	duplication = `Geese::etype_default`
	)

inline

Used when all the functions are in 0 (like the root node prob.)

Needs to specify function a.

Definition at line 1633 of file counters.hpp.

◆ counter_gains_k_offspring()

void counter_gains_k_offspring	(	PhyloCounters *	counters,
		std::vector< size_t >	nfun,
		size_t	k = `1u`,
		size_t	duplication = `Geese::etype_default`
	)

inline

k genes gain function nfun

Definition at line 159 of file counters.hpp.

◆ counter_genes_changing()

void counter_genes_changing	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Keeps track of how many genes are changing (either 0, 1, or 2 if dealing with regular trees.)

Definition at line 231 of file counters.hpp.

◆ counter_k_genes_changing()

void counter_k_genes_changing	(	PhyloCounters *	counters,
		size_t	k,
		size_t	duplication = `Geese::etype_default`
	)

inline

Indicator function. Equals to one if \(k\) genes changed and zero otherwise.

Definition at line 1397 of file counters.hpp.

◆ counter_less_than_p_prop_genes_changing()

void counter_less_than_p_prop_genes_changing	(	PhyloCounters *	counters,
		double	p,
		size_t	duplication = `Geese::etype_default`
	)

inline

Indicator function. Equals to one if \(k\) genes changed and zero otherwise.

< How many genes diverge the parent

Definition at line 1517 of file counters.hpp.

◆ counter_longest()

void counter_longest	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Longest branch mutates (either by gain or by loss)

Definition at line 851 of file counters.hpp.

◆ counter_loss()

void counter_loss	(	PhyloCounters *	counters,
		std::vector< size_t >	nfun,
		size_t	duplication = `Geese::etype_default`
	)

inline

Total count of losses for an specific function.

Definition at line 594 of file counters.hpp.

◆ counter_maxfuns()

void counter_maxfuns	(	PhyloCounters *	counters,
		size_t	lb,
		size_t	ub,
		size_t	duplication = `Geese::etype_default`
	)

inline

Cap the number of functions per gene.

Definition at line 532 of file counters.hpp.

◆ counter_neofun()

void counter_neofun	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Total number of neofunctionalization events.

Needs to specify pairs of function.

Definition at line 1021 of file counters.hpp.

◆ counter_neofun_a2b()

void counter_neofun_a2b	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Total number of neofunctionalization events.

Needs to specify pairs of function.

Definition at line 1166 of file counters.hpp.

◆ counter_overall_changes()

void counter_overall_changes	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Total number of changes. Use this statistic to account for "preservation".

Definition at line 646 of file counters.hpp.

◆ counter_overall_gains()

void counter_overall_gains	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Overall functional gains.

Total number of gains (irrespective of the function).

Definition at line 61 of file counters.hpp.

◆ counter_overall_gains_from_0()

void counter_overall_gains_from_0	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Used when all the functions are in 0 (like the root node prob.)

Needs to specify function a.

Definition at line 1699 of file counters.hpp.

◆ counter_overall_loss()

void counter_overall_loss	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Overall functional loss.

Definition at line 484 of file counters.hpp.

◆ counter_pairwise_first_gain()

void counter_pairwise_first_gain	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Used when all the functions are in 0 (like the root node prob.)

Needs to specify function a. sum x(a)^3(1-x(b))^3 + x(b)^3(1-x(a))^3 + x(a)^3 * x(b)^3 + (1 - x(a))^3 * (1-x(b))^3

Definition at line 1951 of file counters.hpp.

◆ counter_pairwise_neofun_singlefun()

void counter_pairwise_neofun_singlefun	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	duplication = `Geese::etype_default`
	)

inline

Total number of neofunctionalization events sum_u sum_{w < u} [x(u,a)*(1 - x(w,a)) + (1 - x(u,a)) * x(w,a)] change stat: delta{x(u,a): 0->1} = 1 - 2 * x(w,a)

Definition at line 1102 of file counters.hpp.

◆ counter_pairwise_overall_change()

void counter_pairwise_overall_change	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Used when all the functions are in 0 (like the root node prob.)

Needs to specify function a.

Definition at line 1747 of file counters.hpp.

◆ counter_pairwise_preserving()

void counter_pairwise_preserving	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Used when all the functions are in 0 (like the root node prob.)

Needs to specify function a. sum x(a)^3(1-x(b))^3 + x(b)^3(1-x(a))^3 + x(a)^3 * x(b)^3 + (1 - x(a))^3 * (1-x(b))^3

Definition at line 1812 of file counters.hpp.

◆ counter_preserve_pseudogene()

void counter_preserve_pseudogene	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Keeps track of how many pairs of genes preserve pseudostate.

Definition at line 300 of file counters.hpp.

◆ counter_prop_genes_changing()

void counter_prop_genes_changing	(	PhyloCounters *	counters,
		size_t	duplication = `Geese::etype_default`
	)

inline

Keeps track of how many genes are changing (either 0, 1, or 2 if dealing with regular trees.)

Definition at line 382 of file counters.hpp.

◆ counter_subfun()

void counter_subfun	(	PhyloCounters *	counters,
		size_t	nfunA,
		size_t	nfunB,
		size_t	duplication = `Geese::etype_default`
	)

inline

Total count of Sub-functionalization events.

It requires to specify data = {funA, funB}

Definition at line 705 of file counters.hpp.

Modules

Detailed Description

Function Documentation

◆ counter_co_opt()

◆ counter_cogain()

◆ counter_gains()

◆ counter_gains_from_0()

◆ counter_gains_k_offspring()

◆ counter_genes_changing()

◆ counter_k_genes_changing()

◆ counter_less_than_p_prop_genes_changing()

◆ counter_longest()

◆ counter_loss()

◆ counter_maxfuns()

◆ counter_neofun()

◆ counter_neofun_a2b()

◆ counter_overall_changes()

◆ counter_overall_gains()

◆ counter_overall_gains_from_0()

◆ counter_overall_loss()

◆ counter_pairwise_first_gain()

◆ counter_pairwise_neofun_singlefun()

◆ counter_pairwise_overall_change()

◆ counter_pairwise_preserving()

◆ counter_preserve_pseudogene()

◆ counter_prop_genes_changing()

◆ counter_subfun()