/usr/include/JAGS/distribution/RScalarDist.h is in jags 4.3.0-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 | #ifndef R_SCALAR_DIST_H_
#define R_SCALAR_DIST_H_
#include <distribution/ScalarDist.h>
namespace jags {
struct RNG;
/**
* @short Scalar Distribution using R math library infrastructure.
*
* A subclass of RScalarDist has to implement the d,p,q, and r virtual
* member functions. These are based on the d-p-q-r functions provided
* by libRmath.
*
* The JAGS versions of most (but not all) scalar distributions extend
* the distribution families in libRmath by allowing the distribution
* to be bounded.
*/
class RScalarDist : public ScalarDist
{
const bool _discrete;
double calPlower(double, std::vector<double const *> const &) const;
double calPupper(double, std::vector<double const *> const &) const;
public:
/**
* Constructor
*
* @param name BUGS language name of distribution
*
* @param npar Number of parameters, excluding upper and lower bound
*
* @param support Support of distribution
*
* @param discrete Boolean flag indicating whether the distribution is
* discrete valued.
*/
RScalarDist(std::string const &name, unsigned int npar, Support support,
bool discrete=false);
double logDensity(double x, PDFType type,
std::vector<double const *> const ¶meters,
double const *lower, double const *upper) const;
double randomSample(std::vector<double const *> const ¶meters,
double const *lower, double const *upper,
RNG *rng) const;
/**
* Returns the median. Note that this function can be overloaded
* by a subclass if necessary.
*/
double typicalValue(std::vector<double const *> const ¶meters,
double const *lower, double const *upper) const;
/**
* Density function, ignoring bounds
* @param x value at which to evaluate the density
* @param type Type of density calculation required.
* @param parameters Array of parameters
* @param give_log Indicates whether to return log density.
*/
virtual double d(double x, PDFType type,
std::vector<double const *> const ¶meters,
bool give_log) const = 0;
/**
* Distribution function, ignoring bounds
* @param x quantile at which to evaluate the distribution function
* @param parameters Array of parameters
* @param lower If true, return value is P[X <= x]. Otherwise
* P[X > x]
* @param give_log Indicates whether to return log probabability
*/
virtual double p(double x, std::vector<double const *> const ¶meters,
bool lower, bool give_log) const = 0;
/**
* Quantile function, ignoring bounds
* @param p probability for which to evaluate quantile
* @param parameters Array of parameters
* @param log_p Indicates whether p is given as log(p).
*/
virtual double q(double p, std::vector<double const *> const ¶meters,
bool lower, bool log_p) const = 0;
/**
* Random number generation, ignoring bounds
* @param parameters Array of parameters
*/
virtual double
r(std::vector<double const *> const ¶meters, RNG *rng) const = 0;
/**
* All RScalarDist distributions can be bounded
*/
bool canBound() const;
/**
* RScalarDist distributions are defined to have support on the integers
* or on the real line by the constructor
*/
bool isDiscreteValued(std::vector<bool> const &mask) const;
/**
* Alternative function for determining whether the distribution is
* discrete-valued.
*/
bool discrete() const;
};
/**
* Convenience function that calculates x * log(0) as the limit of
* x * log(p) as p tends to zero. This is required for calculation
* of some density functions.
*
* @param x coefficient of log(0)
* @param give_log logical flag. If true then the limit of x*log(p)
* is returned, otherwise the limit of p^x.
*/
double xlog0(double x, bool give_log);
}
#endif /* SCALAR_DIST_RMATH_H_ */
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