Random number generation class, uses various types of random generators depending on the implementation. More...

#include <Uniform.h>

Static Public Member Functions
static void	init (unsigned long seed)
	Initialize the random generator's seed.
static double	Uniform ()
	Generates a random number from [0.0, 1.0[ uniformly distributed.
static unsigned int	Uniform (unsigned int max)
	Returns a uniformly distributed random number from [0.0, max[.
static bool	RandBool ()
	Returns a random boolean.
static unsigned long	RandULong ()
	Return a random unsigned long, from uniform distribution.
static double	gammln (double xx)
	From the Numerical Recieps.
static double	Poisson (double mean)
	From the Numerical Recieps.
static double	Gaussian (double sigma)
	From the GSL.
static void	BivariateGaussian (double sigma1, double sigma2, double rho, double out1, double out2)
static double	LogNormal (double zeta, double sigma)
static double	Gamma (double a, double b)
static double	Exponential (double mu)
Public Attributes
static long	Seed2 = 98280582
Static Public Attributes
static long	Seed1 = 0
Private Member Functions
	RAND ()

Detailed Description

Random number generation class, uses various types of random generators depending on the implementation.

Definition at line 49 of file Uniform.h.

Constructor & Destructor Documentation

RAND::RAND ( ) [private]

Member Function Documentation

static void RAND::BivariateGaussian	(	double	sigma1,
		double	sigma2,
		double	rho,
		double *	out1,
		double *	out2
	)		`[inline, static]`

Definition at line 253 of file Uniform.h.

References Uniform().

                                                                                                           {
#ifdef HAS_GSL
    gsl_ran_bivariate_gaussian(r,sigma1,sigma2,rho,out1,out2);
#else
    //gsl code:
    double u, v, r2, scale;
   //double *x = out, *y = (++out);
    do
    {
      /* choose x,y in uniform square (-1,-1) to (+1,+1) */
      
      u = -1 + 2 * Uniform ();
      v = -1 + 2 * Uniform ();
      
      /* see if it is in the unit circle */
      r2 = u * u + v * v;
    }
    while (r2 > 1.0 || r2 == 0);
    
    scale = sqrt (-2.0 * log (r2) / r2);
    
    *out1 = sigma1 * u * scale;
    *out2 = sigma2 * (rho * u + sqrt(1 - rho*rho) * v) * scale;
    
#endif
  }

static double RAND::Exponential ( double mu ) [inline, static]

Definition at line 316 of file Uniform.h.

References Uniform().

Referenced by TProtoDeletMutations_bitstring::set_effects_exp().

                                               {
    return -mu * log(RAND::Uniform());
  }

static double RAND::Gamma	(	double	a,
		double	b
	)		`[inline, static]`

Definition at line 308 of file Uniform.h.

References fatal().

Referenced by TProtoDeletMutations_bitstring::set_effects_gamma().

                                                  {
#ifdef HAS_GSL
    return gsl_ran_gamma(r, a, b);
#else
    fatal("RAND::Gamma unimplemented; please link with the GNU Scientific Library to get it.");
#endif
  }

static double RAND::gammln ( double xx ) [inline, static]

From the Numerical Recieps.

Definition at line 174 of file Uniform.h.

Referenced by Poisson().

                                          {
    double x,y,tmp,ser=1.000000000190015;
    static double cof[6]={76.18009172947146,-86.50532032941677,
      24.01409824083091,-1.231739572450155,
      0.1208650973866179e-2,-0.5395239384953e-5};
    int j;
    y=x=xx;
    tmp=x+5.5;
    tmp -= (x+0.5)*log(tmp);
    for (j = 0; j < 6; ++j) ser += cof[j]/++y;

    return -tmp+log(2.5066282746310005*ser/x);

  }

static double RAND::Gaussian ( double sigma ) [inline, static]

From the GSL.

Definition at line 227 of file Uniform.h.

References Uniform().

Referenced by LCE_Selection_base::getFitnessMultivariateGaussian_VE(), LCE_Selection_base::getFitnessUnivariateGaussian_VE(), LCE_Breed_base::getGaussianFecundity(), and LCE_Patch_Extinction::rand_gaussian().

  {
#ifdef HAS_GSL
    
    return gsl_ran_gaussian (r, sigma);
    
#else
    double x, y, r2;
    
    do
    {
      /* choose x,y in uniform square (-1,-1) to (+1,+1) */
      
      x = -1 + 2 * Uniform ( );
      y = -1 + 2 * Uniform ( );
      
      /* see if it is in the unit circle */
      r2 = x * x + y * y;
    }
    while (r2 > 1.0 || r2 == 0);
    
    /* Box-Muller transform */
    return sigma * y * sqrt (-2.0 * log (r2) / r2);
#endif
  }

static void RAND::init ( unsigned long seed ) [inline, static]

Initialize the random generator's seed.

Definition at line 77 of file Uniform.h.

References Seed1.

                                        {

#ifdef HAS_GSL
    
    init_gsl( gsl_rng_mt19937, seed );

#elif defined(HAS_SPRNG)
    
    init_sprng( SPRNG_LFG, seed, SPRNG_DEFAULT );
    
#else
    
    Seed1 = seed;
    
#endif
  }

static double RAND::LogNormal	(	double	zeta,
		double	sigma
	)		`[inline, static]`

Definition at line 280 of file Uniform.h.

References Uniform().

Referenced by LCE_Patch_Extinction::rand_lognormal(), and TProtoDeletMutations_bitstring::set_effects_lognorm().

                                                             {
#ifdef HAS_GSL
    return gsl_ran_lognormal(r,zeta,sigma);
#else
    //this is the GSL code:
    double u, v, r2, normal, z;
    
    do
    {
      /* choose x,y in uniform square (-1,-1) to (+1,+1) */
      
      u = -1 + 2 * Uniform();
      v = -1 + 2 * Uniform();
      
      /* see if it is in the unit circle */
      r2 = u * u + v * v;
    }
    while (r2 > 1.0 || r2 == 0);
    
    normal = u * sqrt (-2.0 * log (r2) / r2);
    
    z =  exp (sigma * normal + zeta);
    
    return z;
    
#endif
  }

static double RAND::Poisson ( double mean ) [inline, static]

From the Numerical Recieps.

Definition at line 189 of file Uniform.h.

References gammln(), and Uniform().

Referenced by LCE_Breed_base::getPoissonFecundity(), TTNeutralGenes::inherit_low(), TTNeutralGenes::mutate_KAM(), TTDeletMutations_bitstring::mutate_noredraw(), TTDeletMutations_bitstring::mutate_redraw(), TTNeutralGenes::mutate_SSM(), LCE_Patch_Extinction::rand_poisson(), and TTDeletMutations_bitstring::recombine().

                                             {
    static double sq,alxm,g,oldm=(-1.0);
    double em,t,y;

    if (mean < 12.0)
      {
      if (mean != oldm){
        oldm=mean;
        g=exp(-mean);
      }
      em = -1;
      t=1.0;
      do {
        ++em;
        t *= Uniform();
      } while (t > g);
      }else
        {
        if (mean != oldm)
          {
          oldm=mean;
          sq=sqrt(2.0*mean);
          alxm=log(mean);
          g=mean*alxm-gammln(mean+1.0);
          }
        do {
          do {
            y=tan(M_PI*Uniform());
            em=sq*y+mean;
          } while (em < 0.0);
          em=floor(em);
          t=0.9*(1.0+y*y)*exp(em*alxm-gammln(em+1.0)-g);
        } while (Uniform() > t);
        }
    return em;
  }

static bool RAND::RandBool ( ) [inline, static]

Returns a random boolean.

Definition at line 133 of file Uniform.h.

References Uniform().

Referenced by LCE_Breed_base::getOffsprgSexFixed(), LCE_Breed_base::getOffsprgSexRandom(), TTDeletMutations_bitstring::inherit_0(), TTNeutralGenes::inherit_free(), TTDeletMutations_bitstring::inherit_free(), TTNeutralGenes::inherit_low(), LCE_Disperse_EvolDisp::Migrate_SteppingStone1D(), TTDeletMutations_bitstring::mutate_noredraw(), TTNeutralGenes::mutate_SSM(), TTDeletMutations_bitstring::recombine(), LCE_Breed_Wolbachia::wolbachia_model_1(), and LCE_Breed_Wolbachia::wolbachia_model_2().

                                {
    //generate a random int (or long)
#ifdef HAS_SPRNG
    static int intrand = isprng();
#elif defined(HAS_GSL)
    static unsigned long int intrand =  gsl_rng_get(r);
#else
    static int intrand = (int)(Uniform()*(double)std::numeric_limits<int>::max());
#endif
    //read up to the first 16 bits
    static unsigned int num = 0;
    //redraw an number after that limit
    if ( ++num > 16 ) {
      num = 0;

#ifdef HAS_SPRNG
      intrand = isprng();
#elif defined(HAS_GSL)
      intrand =  gsl_rng_get(r);
#else
      intrand = (int)(Uniform()*(double)std::numeric_limits<int>::max());
#endif

    }
    return (intrand & (1 << num) );

  }

static unsigned long RAND::RandULong ( ) [inline, static]

Return a random unsigned long, from uniform distribution.

Definition at line 161 of file Uniform.h.

References Uniform().

                                          {
#ifdef HAS_GSL
    return gsl_rng_get(r);
#else
    unsigned long rnd, limit = 0x10000000; //=2^28 this gives ~7% redraws
    do{
      rnd = (unsigned long)(Uniform()*ULONG_MAX);
    }while(rnd < limit);

    return rnd;
#endif
  }

static double RAND::Uniform ( ) [inline, static]

Generates a random number from [0.0, 1.0[ uniformly distributed.

If SPRNG or GSL libraries are not used, implement a random generator from: L'Ecuyer, 1988, "Efficient and Portable Combined Random Number Generators", Communication of the ACM, 31(6):742-774.

Definition at line 98 of file Uniform.h.

References Seed1, and Seed2.

Referenced by BivariateGaussian(), LCE_Breed_base::checkPolygyny(), LCE_Selection_base::doViabilitySelection(), LCE_Disperse_EvolDisp::evoldisp(), Exponential(), Metapop::fillPopulationFromSource(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Breed_base::fullPolyginy_manyMales(), Gaussian(), LCE_Breed_Disperse::get_parent(), LCE_Disperse_base::getMigrationPatchBackward(), LCE_Disperse_base::getMigrationPatchForward(), TTNeutralGenes::inherit_low(), TTNeutralGenes::init_sequence(), TTDeletMutations_bitstring::init_sequence(), LogNormal(), LCE_Breed_Selection::makeOffspringWithSelection(), LCE_Breed_Disperse::mate_selfing(), LCE_Disperse_EvolDisp::Migrate_Island(), LCE_Disperse_EvolDisp::Migrate_Island_Propagule(), TTWolbachia::mutate(), TTNeutralGenes::mutate_KAM(), TTDeletMutations_bitstring::mutate_noredraw(), TTDeletMutations_bitstring::mutate_redraw(), TTNeutralGenes::mutate_SSM(), LCE_Breed_base::partialMonoginy(), LCE_Breed_base::partialPolyginy(), LCE_Breed_base::partialPolyginy_manyMales(), LCE_Breed_base::partialSelfing(), Poisson(), LCE_Patch_Extinction::rand_exp(), LCE_Patch_Extinction::rand_uniform(), RandBool(), LCE_Breed_base::random_hermaphrodite(), LCE_Breed_base::RandomMating(), RandULong(), TTDeletMutations_bitstring::recombine(), LCE_Resize::regulateAgeClassNoBackup(), LCE_Resize::regulateAgeClassWithBackup(), LCE_Disperse_base::setPropaguleTargets(), LCE_Selection_base::setSpatialMatrix(), and LCE_Breed_Wolbachia::wolbachia_model_1().

                                  {

#ifdef HAS_SPRNG
    return sprng();
#elif defined(HAS_GSL)
    return gsl_rng_uniform(r);
#else
    register long z, w;

    do{
      w = Seed1 / 53668;

      Seed1 = 40014 * (Seed1 - w * 53668) - w * 12211;

      if (Seed1 < 0) Seed1 += 2147483563;

      w = (Seed2 / 52774);

      Seed2 = 40692 * (Seed2 - w * 52774) - w * 3791;

      if (Seed2 < 0) Seed2 += 2147483399;

      z = Seed1 - Seed2;

      if (z < 1) z += 2147483562;

    }while (!((z * 4.656613e-10) < 1.0));

    return (z * 4.656613e-10);
#endif
  }

static unsigned int RAND::Uniform ( unsigned int max ) [inline, static]

Returns a uniformly distributed random number from [0.0, max[.

Definition at line 130 of file Uniform.h.

References Uniform().

Referenced by Uniform().

{return (unsigned int)(Uniform() * max);}

Member Data Documentation

long RAND::Seed1 = 0 [static]

Definition at line 73 of file Uniform.h.

Referenced by init(), and Uniform().

long RAND::Seed2 = 98280582

Definition at line 73 of file Uniform.h.

Referenced by Uniform().

The documentation for this class was generated from the following files:

Static Public Member Functions

Public Attributes

Static Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation