Predefined PDFs

##Univariate Discrete Distributions

Functions	Emission Function Name	Parameters
binomial_pdf (int k, int n, double p)	BINOMIAL	2
beta_binomial_pdf (int k, int n, double a, double b)	BETA_BINOMIAL	3
degenerate_pdf ( double value, double k)	DEGENERATE	1
discrete_uniform_pdf (int position, int a, int b)	DISCRETE_UNIFORM	2
hypergeometric_pdf (int k, int n, int N, int m)	HYPERGEOMETRIC	3
beta_negative_binomial_pdf (int k, int n, double a, double b)	BETA_NEGATIVE_BINOMIAL	3
maxwell_boltzman_pdf ( x, double a)	MAXWELL_BOLTZMAN	1
geometric_pdf (int k, double p)	GEOMETRIC	1
logarithmic_pdf (int k, double p)	LOGARITHMIC	1
negative_binomial_pdf (int k, int r, double p)	NEGATIVE_BINOMIAL	2
poisson_pdf (int k, double lambda)	POISSON	1
yule_simon_pdf (int k, double p)	YULE_SIMON	1
zipf_pdf (int k, int N, double s)	ZIPF	2
zipf_mandelbrot_pdf (int k, int N, double s, double q)	ZIPF-MANDELBROT	3

##Univariate Continuous Distributions

Functions	Emission Function Name	Parameters
arcsine_pdf ( double x)	ARCSINE	0
beta_pdf (double x, double a, double b)	BETA	2
logit_normal_pdf (double x, double mu, double sigma)	LOGIT_NORMAL	2
continuous_uniform_pdf (double x, double a, double b)	CONTINUOUS_UNIFORM	2
kumaraswamy_pdf (double x, double a, double b)	KUMARASWAMY	2
raised_cosine_pdf (double x, double mu, double s)	RAISED_COSINE	2
triangular_pdf (double x, double a, double b, double c)	TRIANGULAR	3
truncated_normal_pdf (double x, double mu, double sd, double a, double b)	TRUNCATED_NORMAL	4
u_quadratic_pdf (double x, double a, double b)	U_QUADRATIC	2
wigner_semicircle_pdf (double x, double r)	WIGNER_SEMICIRCLE	1
beta_prime_pdf (double x, double a, double b)	BETA_PRIME	2
chi_pdf (double x, double k)	CHI	1
chi_squared_pdf (double x, double k)	CHI_SQUARED	1
inverse_chi_squared_pdf (double x, double v)	INVERSE_CHI_SQUARED	1
scaled_inverse_chi_squared_pdf (double x, double v, double sigma_sqrd)	SCALED_INVERSE_CHI_SQUARED	2
dagum_pdf (double x, double p, double a, double b)	DAGUM	3
exponential_pdf (double x, double lambda)	EXPONENTIAL	1
f_pdf (double x, double d1, double d2)	F_DIST	2
fishers_z_pdf (double x, double d1, double d2)	FISHERS_Z	2
folded_normal_pdf (double x, double mu, double sigma_sqrd)	FOLDED_NORMAL	3
frechet_pdf (double x, double alpha, double s, double m)	FRECHET	3
gamma_pdf (double x, double alpha, double beta)	GAMMA	2
inv_gamma_pdf (double x, double alpha, double beta)	INVERSE_GAMMA	2
half_normal_pdf (double x, double sigma)	HALF_NORMAL	1
inv_gaussian_pdf (double x, double mu, double lambda)	INVERSE_GAUSSIAN	2
levy_pdf (double x, double mu, double scale)	LEVY	2
log_cauchy_pdf (double x, double mu, double sigma)	LOG_CAUCHY	2
log_laplace_pdf (double x, double mu, double b)	LOG_LAPLACE	2
log_logistic_pdf (double x, double a, double b)	LOG_LOGISTIC	2
log_normal_pdf (double x, double mu, double sigma_sqrd)	LOG_NORMAL	2
pareto_pdf (double x, double alpha, double x_m)	PARETO	2
nakagami_pdf (double x, double mu, double w)	NAKAGAMI	2
rayleigh_pdf (double x, double sigma)	RAYLEIGH	1
gumbel_type_two_pdf (double x, double a, double b)	GUMBEL_TYPE_TWO	2
weibull_distribution (double x, double lambda, double k)	WEIBULL	2
cauchy_pdf (double x, double x_o, double gamma)	CAUCHY	2
gumbel_pdf (double x, double mu, double beta)	GUMBEL	2
generalized_normal_pdf (double x, mu, alpha, beta)	GENERALIZED_NORMAL	3
hyperbolic_secant_pdf (double x)	HYPERBOLIC_SECANT	0
laplace_pdf (double x, double mu, double b)	LAPLACE	2
logistic_pdf (double x, double mu, double s)	LOGISTIC	2
standard_normal_pdf (double x)	STANDARD_NORMAL	0
normal_pdf (double x, double mu, double sigma)	NORMAL	2
students_t_pdf (double x, double v)	STUDENT_T	1
gumbel_type_one_pdf (double x, double a, double b)	GUMBEL_TYPE_ONE	2
generalized_extreme_value_pdf (double x, double mu, double sigma, double xi)	GENERALIZED_EXTREME_VALUE	3
generalized_pareto_pdf (double x, double mu, double sigma, double xi)	GENERALIZED_PARETO	3

##Multivariate Continuous Distributions

Functions	Emission Function Name	Parameters
dirichlet_pdf (const std::vector& x,const std::vector&alpha)	DIRICHLET	Same as # of variables
multivariate_ewens_pdf(const std::vector& x, const double theta)	EWENS	1

#List of Probability Distribution Function (PDF.h and PDF.cpp)

###Univariate Discrete Distributions

double 	StochHMM::binomial_pdf (int k, int n, double p)
double 	StochHMM::beta_binomial_pdf (int k, int n, double a, double b)
double 	StochHMM::degenerate_pdf (double value, double k)
double 	StochHMM::discrete_uniform_pdf (int position, int a, int b)
double 	StochHMM::hypergeometric_pdf (int k, int n, int N, int m)
double 	StochHMM::poisson_binomial_pdf (int k, std::vector< double > &p)
double 	StochHMM::beta_negative_binomial_pdf (int k, int n, double a, double b)
double 	StochHMM::maxwell_boltzman_pdf (double x, double a)
double 	StochHMM::geometric_pdf (int k, double p)
double 	StochHMM::logarithmic_pdf (int k, double p)
double 	StochHMM::negative_binomial_pdf (int k, int r, double p)
double 	StochHMM::poisson_pdf (int k, double lambda)
double 	StochHMM::yule_simon_pdf (int k, double p)
double 	StochHMM::zipf_pdf (int k, int N, double s)
double 	StochHMM::zipf_mandelbrot_pdf (int k, int N, double s, double q)

###Univariate Continuous Distributions

double 	StochHMM::arcsine_pdf (double x)
double 	StochHMM::beta_pdf (double x, double a, double b)
double 	StochHMM::logit_normal_pdf (double x, double mu, double sigma)
double 	StochHMM::continuous_uniform_pdf (double x, double a, double b)
double 	StochHMM::kumaraswamy_pdf (double x, double a, double b)
double 	StochHMM::raised_cosine_pdf (double x, double mu, double s)
double 	StochHMM::triangular_pdf (double x, double a, double b, double c)
double 	StochHMM::truncated_normal_pdf (double x, double mu, double sd, double a, double b)
double 	StochHMM::u_quadratic_pdf (double x, double a, double b)
double 	StochHMM::wigner_semicircle_pdf (double x, double r)
double 	StochHMM::beta_prime_pdf (double x, double a, double b)
double 	StochHMM::chi_pdf (double x, double k)
double 	StochHMM::chi_squared_pdf (double x, double k)
double 	StochHMM::inverse_chi_squared_pdf (double x, double v)
double 	StochHMM::scaled_inverse_chi_squared_pdf (double x, double v, double sigma_sqrd)
double 	StochHMM::dagum_pdf (double x, double p, double a, double b)
double 	StochHMM::exponential_pdf (double x, double lambda)
double 	StochHMM::f_pdf (double x, double d1, double d2)
double 	StochHMM::fishers_z_pdf (double x, double d1, double d2)
double 	StochHMM::folded_normal_pdf (double x, double mu, double sigma_sqrd)
double 	StochHMM::frechet_pdf (double x, double alpha, double s, double m)
double 	StochHMM::gamma_pdf (double x, double alpha, double beta)
double 	StochHMM::inv_gamma_pdf (double x, double alpha, double beta)
double 	StochHMM::half_normal_pdf (double x, double sigma)
double 	StochHMM::inv_gaussian_pdf (double x, double mu, double lambda)
double 	StochHMM::levy_pdf (double x, double mu, double scale)
double 	StochHMM::log_cauchy_pdf (double x, double mu, double sigma)
double 	StochHMM::log_laplace_pdf (double x, double mu, double b)
double 	StochHMM::log_logistic_pdf (double x, double a, double b)
double 	StochHMM::log_normal_pdf (double x, double mu, double sigma_sqrd)
double 	StochHMM::pareto_pdf (double x, double alpha, double x_m)
double 	StochHMM::nakagami_pdf (double x, double mu, double w)
double 	StochHMM::rayleigh_pdf (double x, double sigma)
double 	StochHMM::gumbel_type_two_pdf (double x, double a, double b)
double 	StochHMM::weibull_distribution (double x, double lambda, double k)
double 	StochHMM::cauchy_pdf (double x, double x_o, double gamma)
double 	StochHMM::gumbel_pdf (double x, double mu, double beta)
double 	StochHMM::generalized_normal_pdf (double x, double mu, double alpha, double beta)
double 	StochHMM::hyperbolic_secant_pdf (double x)
double 	StochHMM::laplace_pdf (double x, double mu, double b)
double 	StochHMM::logistic_pdf (double x, double mu, double s)
double 	StochHMM::standard_normal_pdf (double x)
double 	StochHMM::normal_pdf (double x, double mu, double sigma)
double 	StochHMM::students_t_pdf (double x, double v)
double 	StochHMM::gumbel_type_one_pdf (double x, double a, double b)
double 	StochHMM::generalized_extreme_value_pdf (double x, double mu, double sigma, double xi)
double 	StochHMM::generalized_pareto_pdf (double x, double mu, double sigma, double xi)

###Multivariate Distributions

double 	StochHMM::dirichlet_pdf (const std::vector< double > &x, const std::vector< double > &alpha)
double 	StochHMM::multivariate_ewens_pdf (const std::vector< double > &x, double theta)

##Overloaded Functions for use with StochHMM::StateFuncs ###Univariate Discrete Distributions

double 	StochHMM::binomial_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::beta_binomial_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::degenerate_pdf (const double value, const std::vector< double > *param)
double 	StochHMM::discrete_uniform_pdf (const double position, const std::vector< double > *param)
double 	StochHMM::hypergeometric_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::beta_negative_binomial_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::maxwell_boltzman_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::geometric_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::logarithmic_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::negative_binomial_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::poisson_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::yule_simon_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::zipf_pdf (const double k, const std::vector< double > *param)
double 	StochHMM::zipf_mandelbrot_pdf (const double k, const std::vector< double > *param)

###Univariate Continuous Distributions

double 	StochHMM::arcsine_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::beta_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::logit_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::continuous_uniform_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::kumaraswamy_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::raised_cosine_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::triangular_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::truncated_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::u_quadratic_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::wigner_semicircle_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::beta_prime_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::chi_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::chi_squared_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::inverse_chi_squared_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::scaled_inverse_chi_squared_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::dagum_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::exponential_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::f_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::fishers_z_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::folded_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::frechet_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::gamma_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::inv_gamma_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::half_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::inv_gaussian_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::levy_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::log_cauchy_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::log_laplace_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::log_logistic_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::log_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::pareto_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::nakagami_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::rayleigh_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::gumbel_type_two_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::weibull_distribution (const double x, const std::vector< double > *param)
double 	StochHMM::cauchy_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::gumbel_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::generalized_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::hyperbolic_secant_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::laplace_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::logistic_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::standard_normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::normal_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::students_t_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::gumbel_type_one_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::generalized_extreme_value_pdf (const double x, const std::vector< double > *param)
double 	StochHMM::generalized_pareto_pdf (const double x, const std::vector< double > *param)

###Multivariate Continuous Distributions

double dirichlet_multi_pdf(const std::vector<double>* x, const std::vector<double>* param)
double ewens_multi_pdf(const std::vector<double>* x, const std::vector<double>* param)