SHIBA main header More...

#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <ctype.h>
#include <math.h>
#include <pthread.h>
#include <string.h>
#include <time.h>
#include "version.h"

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Data Structures
struct	config
	The structure that stores the configuration information. More...

struct	phylo
	A general phylogeny structure returned from pasring Newick. More...

Macros
#define	_GNU_SOURCE
	to allow the very useful asprintf()

#define	Sasprintf(write_to,...)
	Safer asprintf macro for extending strings.

Functions
void	readArgs (int argc, char **argv)
	Parses arguments to the executable.

void	readXML ()
	Open file and parse XML.

void	printIndata ()
	Output matrices for checking by user.

phylo	parseNewick (char *in)

void	phyloToLineage (phylo p)
	Reconciles the phylogeny edges with the geo time periods

void	help ()
	Default help output.

void	error (char *a)
	Basic error output and exit function.

int *	mem1d_i (int dimx)
	Dimensions an initialized 1-D array of int.

double *	mem1d_d (int dim)
	Dimensions an initialized 1-D array of doubles.

int **	mem2d_i (int dimx, int dimy)
	Dimensions an initialized 2-D array of int.

void	free2d_i (int **ptr, int dimx)

int **	mem2d1_i (int dimx)
	Dimensions a initialized 1-D array of int pointers, ready to be allocated using mem1d_i() .

void	free2d1_i (int **ptr, int dimx)
	Frees the ragged array allocated by mem2d1_i().

double **	mem2d_d (int dimx, int dimy)
	Dimensions an initialized 2-D array of doubles.

void	free2d_d (double **ptr, int dimx)

char **	mem2d1_c (int dimx)
	Dimensions a initialized 1-D array of character pointers, ready to be allocated using asprintf.

void	free2d1_c (char **ptr, int dimx)
	Frees the ragged array allocated by mem2d1_c().

double ***	mem3d_d (int dimx, int dimy, int dimz)
	Dimensions an initialized 3-D array of doubles.

void	free3d_d (double ***ptr, int dimx, int dimy)

int ***	mem3d_i (int dimx, int dimy, int dimz)
	Dimensions an initialized 3-D array of int.

void	free3d_i (int ***ptr, int dimx, int dimy)

void	shiba (phylo p)

double	findMaxArea ()

double	findMaxDist ()

void *	biogeo ()

void	printSuccessAll (phylo p)

double	pDispersal (double x)

double	pSurvival (double x)

void	printArray (int t)

Variables
config	Cfg
	The main config structure.

int	Times
	The number of time periods.

double *	RealTime
	The age of the start of the period.

int	Spaces
	The number of spatial units.

char **	SpaceName
	The names of the spatial area.

int	Phylos
	The number of phylogenies.

char **	Phylo
	The phylogeny strings.

int	Taxa
	The number of terminal taxa.

char **	Taxon
	Terminal taxa names.

double **	Area
	The areas of spates at each time: Area[Time][Space].

double ***	Dist
	The distances among spaces at each time.

double **	PSurv
	The prob of survival PSurv[Time][Space].

double ***	PDisp
	The prob of dispersal PDisp[Time][Space].

int ***	Extant
	0/1 indcating the existance of a taxon or fossil during a particular time period. Care is needed in assigning fossils to periods, due to reconciliation stage. [x][t][s]

int	Lineages
	The number of lineages = phylo.nnodes.

int **	LineagePeriod
	The 0/1 existence of a lineage in a time period.

int **	LineageDaughters
	The daughters of each lineage.

int *	LineageDaughtersN
	The number of daughters of each lineage.

int ***	LineageExtant
	Whether each lineage is extant.

int	LinExtantN
	The number of lineages extant at present.

char *	DataFile
	Name of the data file.

int	PhyloToUse
	Index number of the phylogeny currently in use.

int	PrintData
	Switch 0/1 to control output of raw data.

int **	record

long int	success

long int	topresent

double	maxdist

double	maxarea

pthread_mutex_t	mymutex

int	RUN_BATCH
	the number of threads to run in parallel

Detailed Description

SHIBA main header

Definition in file shiba.h.

Macro Definition Documentation

#define Sasprintf	(	write_to,
		...
	)

Value:

{          \
  char *tmp_string_for_extend = (write_to); \
  asprintf(&(write_to), __VA_ARGS__);       \
  free(tmp_string_for_extend);              \
  }

Safer asprintf macro for extending strings.

From 21st Century C.

Definition at line 13 of file shiba.h.

Referenced by parseNewick(), and readXML().

Function Documentation

void error ( char * error_msg )

Basic error output and exit function.

Note that no freeing is done, possibly leading to memory leaks.

Parameters

error_msg the error message

Definition at line 612 of file io.c.

Referenced by main(), mem1d_d(), mem1d_i(), mem2d1_c(), mem2d1_i(), mem2d_d(), mem2d_i(), mem3d_d(), mem3d_i(), parseNewick(), phyloToLineage(), readArgs(), and readXML().

void free2d1_c	(	char **	ptr,
		int	dimx
	)

Frees the ragged array allocated by mem2d1_c().

Parameters

dimx	The dimensions of the vector

Definition at line 700 of file io.c.

Referenced by main(), and readXML().

void free2d1_i	(	int **	ptr,
		int	dimx
	)

Frees the ragged array allocated by mem2d1_i().

Parameters

dimx	The dimensions of the vector

Definition at line 670 of file io.c.

Referenced by main().

double* mem1d_d ( int dimx )

Dimensions an initialized 1-D array of doubles.

To free, just use free().

Parameters

dimx	The dimensions of the vector

Returns: A pointer to an array of doubles

Definition at line 628 of file io.c.

References error().

Referenced by parseNewick(), and readXML().

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int* mem1d_i ( int dimx )

Dimensions an initialized 1-D array of int.

To free, just use free().

Parameters

dimx	The dimensions of the vector

Returns: A pointer to an array of ints

Definition at line 643 of file io.c.

References error().

Referenced by parseNewick(), phyloToLineage(), and readXML().

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char** mem2d1_c ( int dimx )

Dimensions a initialized 1-D array of character pointers, ready to be allocated using asprintf.

The result will be a `ragged' matrix. To free, use free2d1_c() .

Parameters

dimx	The dimensions of the vector

Returns: A pointer to an array of character pointers

Definition at line 685 of file io.c.

References error().

Referenced by parseNewick(), and readXML().

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int** mem2d1_i ( int dimx )

Dimensions a initialized 1-D array of int pointers, ready to be allocated using mem1d_i() .

The result will be a `ragged' matrix. To free, use free2d1_i() .

Parameters

dimx	The dimensions of the vector

Returns: A pointer to an array of int pointers

Definition at line 658 of file io.c.

References error().

Referenced by phyloToLineage().

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double** mem2d_d	(	int	dimx,
		int	dimy
	)

Dimensions an initialized 2-D array of doubles.

Free with free2d_d()

Definition at line 736 of file io.c.

References error().

Referenced by readXML().

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int** mem2d_i	(	int	dimx,
		int	dimy
	)

Dimensions an initialized 2-D array of int.

Free with free2d_i()

Definition at line 712 of file io.c.

References error().

Referenced by phyloToLineage().

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double*** mem3d_d	(	int	dimx,
		int	dimy,
		int	dimz
	)

Dimensions an initialized 3-D array of doubles.

Free with free3d_d()

Definition at line 760 of file io.c.

References error().

Referenced by readXML().

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int*** mem3d_i	(	int	dimx,
		int	dimy,
		int	dimz
	)

Dimensions an initialized 3-D array of int.

Free with free3d_i()

Definition at line 793 of file io.c.

References error().

Referenced by phyloToLineage(), and readXML().

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phylo parseNewick ( char * in )

Todo:: deal with quoted labels

Definition at line 7 of file newick.c.

References phylo::age, phylo::bl, phylo::depth, error(), mem1d_d(), mem1d_i(), mem2d1_c(), phylo::ndaughter, phylo::nnodes, phylo::parent, Sasprintf, and phylo::taxon.

Referenced by main().

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void phyloToLineage ( phylo p )

Reconciles the phylogeny edges with the geo time periods

For example, imagine three past time periods (A, B, C) and the future (Z), and several phylogeny edges (a-k):

 Z :   a     b   d     e   g     h    j     
 ..:...|.....|...|.....|...|.....|....|..... NOW
   :   |     |   |     |   +--+--+    |
 C :   +--+--+   |     |      |i      |
   :      |c     |     |      +----+--+
 ..:......|......|.....|...........|........
   :      |      +--+--+           |k
 B :      |         |f             |
 ..:......|.........|..............|........
 A :      |         |              |

These would be encoded with reference to the time periods as:

          a b c    d e f    g h i j k
          -----    -----    ---------
      Z | 1 1 0    1 1 0    1 1 x 1 0
      C | 0 0 1    1 1 0    0 0 x 0 1
      B | 0 0 1    0 0 1    0 0 x 0 1
      A | 0 0 1    0 0 1    0 0 x 0 1

Note that we need to push the branching events `forward,' so that there is only ever one root stem passing through the beginning of the first time period.

Definition at line 199 of file newick.c.

References phylo::age, phylo::bl, error(), Extant, LineageDaughters, LineageDaughtersN, LineageExtant, LineagePeriod, Lineages, mem1d_i(), mem2d1_i(), mem2d_i(), mem3d_i(), phylo::ndaughter, phylo::nnodes, phylo::parent, RealTime, Spaces, Taxa, phylo::taxon, Taxon, and Times.