A single segment of a population tree. More...

#include "popnode.h"
#include "gene.h"
#include "misc.h"
#include "parstore.h"
#include "ptrptrmap.h"
#include "error.h"
#include <stdbool.h>
#include <string.h>
#include <float.h>
#include <math.h>
#include <gsl/gsl_randist.h>

Data Structures
struct	PopNode

Functions
static void	PopNode_transferSample (PopNode self, Gene gene)
	Transfer an existing sample to a PopNode.

static void	PopNode_printShallow (PopNode self, FILE fp)
	Print a PopNode but not its descendants.

static void	PopNode_sanityCheck (PopNode self, const char file, int lineno)
	Check sanity of PopNode.

static void	PopNode_sanityFromLeaf (PopNode self, const char file, int line)
	Check for errors in PopNode tree. Call this from each leaf node.

static int	PopNode_nsamples (PopNode *self)
	Return the number of samples in a PopNode.

static void	PopNode_duplicate_nodes (PopNode old, PtrPtrMap ppm)
	Traverse tree, making a duplicate of each node, and putting the duplicates into a hash map (called ppm) in which the old node is the key and the new duplicate is the value associated with that key.

static void	unlink_child (PopNode child, PopNode parent)
	Remove child from parent.

static int	PopNode_equals_r (PopNode a, PopNode b)

static void	PopNode_print_r (PopNode self, FILE fp, int indent)
	Print a PopNode and (recursively) its descendants.

int	PopNode_equals (PopNode a, PopNode b)

void *	PopNode_root (void *vself)
	Find root of population network, starting from given node.

void	PopNode_clear (PopNode *self)
	Remove all references to samples from tree of populations. More...

int	PopNode_isClear (const PopNode *self)
	Return 1 if PopNode tree is empty of samples.

void	PopNode_print (void vroot, FILE fp, int indent)
	Print a network of PopNodes.

void	PopNode_unvisit (PopNode *self)
	Set all "visited" flags to false.

void *	PopNode_new (int twoN_i, int start_i, ParStore ps, const char label)
	PopNode constructor.

void	PopNode_update (PopNode self, ParStore ps)

int	PopNode_addChild (void vparent, void vchild)
	Connect parent and child.

void	PopNode_newSample (PopNode *self, unsigned ndx)
	Allocates a new Gene and puts it into the array within PopNode. More...

int	PopNode_mix (void vchild, int mix_i, void vintrogressor, void vnative, ParStore ps)
	Connect a child PopNode to two parents. More...

Gene *	PopNode_coalesce (PopNode self, gsl_rng rng, long unsigned *event_counter)
	Coalesce gene tree within population tree.

void	PopNode_free (PopNode *self)
	Free node and descendants.

int	PopNode_feasible (const PopNode *self, Bounds bnd, int verbose)
	Return 1 if parameters satisfy inequality constraints, or 0 otherwise.

PopNode *	PopNode_dup (PopNode old_root, PtrPtrMap ppm)
	Duplicate a network of nodes, returning a pointer to the root of the duplicate network. More...

Detailed Description

A single segment of a population tree.

Author: Alan R. Rogers

PopNode objects can be linked together into a network, which models bifurcation of populations and gene flow among them. Each PopNode knows its size and duration. It has pointers to parents and children. If it has two parents, there is also a mixing parameter, which determines what fraction of the node derives from each parent.

Copyright: Copyright (c) 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

◆ PopNode_clear()

void PopNode_clear ( PopNode * self )

Remove all references to samples from tree of populations.

Doesn't free the Gene objects, because they aren't owned by PopNode. Sets "visited" to 0 in every node.

Referenced by GPTree_brlen(), GPTree_free(), and PopNode_dup().

◆ PopNode_dup()

PopNode * PopNode_dup	(	PopNode *	old_root,
		PtrPtrMap *	ppm
	)

Duplicate a network of nodes, returning a pointer to the root of the duplicate network.

On entry, ppm should be an empty hashmap.

References PopNode_clear(), and PopNode_duplicate_nodes().

◆ PopNode_mix()

int PopNode_mix	(	void *	vchild,
		int	mix_i,
		void *	vintrogressor,
		void *	vnative,
		ParStore *	ps
	)

Connect a child PopNode to two parents.

Parameters

[in,out]	child	pointer to the child PopNode
[in]	mPtr	pointer to the gene flow variable
[in,out]	introgressor	pointer to the introgressing parent
[in,out]	native	pointer to the native parent

◆ PopNode_newSample()

void PopNode_newSample	(	PopNode *	self,
		unsigned	ndx
	)

Allocates a new Gene and puts it into the array within PopNode.

The gene isn't owned by PopNode, however. It will eventually be freed by a recursive call to Gene_free, which will free the root Gene and all descendants.

References Gene_new().