gptree.c File Reference

Methods for simulating gene genealogies within a given tree of populations, and allowing populations to mix and also to split. More...

#include "gene.h"
#include "gptree.h"
#include "lblndx.h"
#include "parse.h"
#include "param.h"
#include "parstore.h"
#include "ptrptrmap.h"
#include "sampndx.h"
#include <errno.h>
#include <gsl/gsl_rng.h>
#include <string.h>
#include <unistd.h>
#include <pthread.h>

Data Structures
struct	GPTree
	GPTree stands for Gene-Population tree. More...

Functions
int	GPTree_equals (const GPTree *lhs, const GPTree *rhs)
	Return 1 if two GPTree objects are equal, 0 if they differ. More...
void	GPTree_print (void *vself, FILE *fp)
void	GPTree_initStateVec (void *gpt, int ndx, int n, double x[n], gsl_rng *rng)
	Initialize vector x. More...
void	GPTree_printParStore (void *vself, FILE *fp)
	Print a description of parameters.
void	GPTree_printParStoreFree (void *vself, FILE *fp)
	Print a description of free parameters.
const char *	GPTree_getNameFree (void *self, int i)
	Return pointer to name of i'th free parameter.
void	GPTree_randomize (void *vself, gsl_rng *rng)
	Randomly perturb all free parameters while maintaining inequality constraints.
int	GPTree_setParams (void *vself, int n, double x[n])
	Set free parameters from an array. More...
void	GPTree_getParams (void *self, int n, double x[n])
	Copy free parameters from GPTree into an array. More...
int	GPTree_nFree (const void *self)
	Return number of free parameters.
void	GPTree_brlen (void *vself, BranchTab *branchtab, gsl_rng *rng, unsigned long nreps, int doSing, long unsigned *event_counter)
	Use coalescent simulation to estimate the mean branch length associated with each site pattern. More...
void *	GPTree_new (const char *fname, Bounds bnd)
	GPTree constructor.
void	GPTree_free (void *vself)
	GPTree destructor.
void *	GPTree_dup (const void *vold)
	Duplicate a GPTree object.
void	GPTree_sanityCheck (void *vself, const char *file, int line)
LblNdx	GPTree_getLblNdx (void *vself)
	Get the LblNdx object from a GPTree.
unsigned	GPTree_nsamples (const void *vself)
int	GPTree_feasible (const void *vself, int verbose)
	Are parameters within the feasible region?
unsigned	GPTree_nSamples (void *vself)

Variables
pthread_mutex_t	outputLock

Detailed Description

Methods for simulating gene genealogies within a given tree of populations, and allowing populations to mix and also to split.

Author

Alan R. Rogers

Copyright

Copyright (c) 2016, Alan R. Rogers roger.nosp@m.s@an.nosp@m.thro..nosp@m.utah.nosp@m..edu. This file is released under the Internet Systems Consortium License, which can be found in file "LICENSE".

Function Documentation

GPTree_brlen()

void GPTree_brlen	(	void *	vself,
		BranchTab *	branchtab,
		gsl_rng *	rng,
		unsigned long	nreps,
		int	doSing,
		long unsigned *	event_counter
	)

Use coalescent simulation to estimate the mean branch length associated with each site pattern.

Parameters

	self	GPTree object
[out]	branchtab	BranchTab object, which will tabulate branch lengths from this simulations.
[in,out]	rng	GSL random number generator
[in]	nreps	number of replicate gene trees to simulate
[in]	doSing	if doSing is non-zero, singleton site patterns will be tabulated.

References PopNode_clear().

GPTree_equals()

int GPTree_equals	(	const GPTree *	lhs,
		const GPTree *	rhs
	)

Return 1 if two GPTree objects are equal, 0 if they differ.

Abort with an error if the GPTree pointers are different but one or more of the internal pointers is the same. Does not access rootPop or rootGene. Used for testing GPTree_dup.

GPTree_getParams()

void GPTree_getParams	(	void *	self,
		int	n,
		double	x[n]
	)

Copy free parameters from GPTree into an array.

Parameters

[out]	n	number of parameters in array, which should equal the number of free parameters in the GPTree.
[out]	x	array into which parameters will be copied

References ParStore_getFreeParams().

Referenced by GPTree_initStateVec(), and Network_init().

GPTree_initStateVec()

void GPTree_initStateVec	(	void *	gpt,
		int	ndx,
		int	n,
		double	x[n],
		gsl_rng *	rng
	)

Initialize vector x.

If ndx==0, simply copy the parameter vector from the GPTree object. Otherwise, randomize the GPTree first. This ensures that differential evolution starts with a set of points, one of which is the same as the values in the input file. This allows you to improve on existing estimates without starting from scratch each time.

References GPTree_dup(), GPTree_free(), GPTree_getParams(), and GPTree_randomize().

GPTree_setParams()

int GPTree_setParams	(	void *	vself,
		int	n,
		double	x[n]
	)

Set free parameters from an array.

Parameters

[in]	n	number of parameters in array, which should equal the number of free parameters in the GPTree.
[in]	x	array of parameter values.

Returns

0 on success, 1 if values of x violate boundary constraints.

References ParStore_nFree(), and ParStore_setFreeParams().