boot.h File Reference

Header for boot.c. More...

#include "typedefs.h"
#include <gsl/gsl_rng.h>

Go to the source code of this file.

Macros
#define	DEF_BOOT_BLOCK_SIZE   500

Functions
Boot *	Boot_new (int nchr, long nsnp[nchr], long nrep, int npat, long blocksize, gsl_rng *rng)
	Constructor for class Boot.
void	Boot_free (Boot *self)
	Destructor.
void	Boot_add (Boot *self, int chr, long snpndx, int pat, double z)
	Add one site pattern contribution to a Boot structure. More...
void	Boot_aggregate (Boot *self, int rep, int npat, double count[npat])
	Add to an array the site pattern counts from a bootstrap replicate. More...
void	Boot_print (const Boot *self, FILE *ofp)
	Print a Boot object.
void	Boot_sanityCheck (const Boot *self, const char *file, int line)
void	confidenceBounds (double *lowBnd, double *highBnd, double confidence, long len, double v[len])
	Calculate confidence bounds from a vector of values representing samples drawn from the sampling distribution of some estimator. More...
unsigned	Boot_multiplicity_slow (Boot *self, long snp, long rep)

Detailed Description

Header for boot.c.

Author

Alan R. Rogers

Copyright

Copyright (c) 2016,2018 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

Boot_add()

void Boot_add	(	Boot *	self,
		int	chr,
		long	snpndx,
		int	pat,
		double	z
	)

Add one site pattern contribution to a Boot structure.

Parameters

[in,out]	self	The Boot structure to modify.
[in]	chr	The index of the chromosome to modify.
[in]	snpndx	The index of the current snp.
[in]	pat	The index of the current site pattern.
[in]	z	the contribution of the snp to the site pattern.

References Boot_multiplicity(), Boot::count, Boot::cum, and Boot::nrep.

Boot_aggregate()

void Boot_aggregate	(	Boot *	self,
		int	rep,
		int	npat,
		double	count[npat]
	)

Add to an array the site pattern counts from a bootstrap replicate.

Parameters

[in]	self	Points to a Boot object.
[in]	the	index of the bootstrap replicate
[in]	npat	the number of site patterns
[out]	count	An array of doubles. The function will add to count[i] the contribution of site pattern i in bootstrap replicate rep.

References Boot::npat.

confidenceBounds()

void confidenceBounds	(	double *	lowBnd,
		double *	highBnd,
		double	confidence,
		long	len,
		double	v[len]
	)

Calculate confidence bounds from a vector of values representing samples drawn from the sampling distribution of some estimator.

To calculate the lower bound (*lowBnd), the function calculates the total probability mass in the tails (1 - confidence) and divides this into two equal parts to find p, the probability mass in each tail. It then estimates a value L such that a fraction p of the data values are less than or equal to L. To find this value, the function uses linear interpolation between the sorted list of data values.

The upper bound (*highBnd) is calculated in an analogous fashion.

Parameters

[out]	lowBnd,highBnd	Calculated results will be written into these memory locations.
[in]	confidence	Fraction of sampling distribution that lies inside the confidence bounds.
[in]	len	The number of values inf v.
[in]	v	The vector of values.

Side Effects:\n Sorts the vector v.