/usr/include/JAGS/sampler/RWMetropolis.h is in jags 3.4.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #ifndef RW_METROPOLIS_H_
#define RW_METROPOLIS_H_
#include <sampler/Metropolis.h>
#include <sampler/StepAdapter.h>
/**
* @short Random Walk Metropolis-Hastings sampling method
*
* This class provides an update function which modifies the current
* value by a random walk. This step size is adapted to achieve the
* target acceptance rate using a noisy gradient algorithm.
*/
class RWMetropolis : public Metropolis
{
StepAdapter _step_adapter;
double _pmean;
unsigned int _niter;
public:
/**
* Constructor.
*
* @param value Initial value vector.
* @param step Initial step size for the random walk updates.
* @param prob Target acceptance probability. The default seems to
* be a fairly robust optimal value.
*/
RWMetropolis(std::vector<double> const &value, double step,
double prob = 0.234);
~RWMetropolis();
/**
* Updates the current value by adding a random increment.
*/
void update(RNG *rng);
/**
* Modifies the step size to achieve the target acceptance
* probability using a noisy gradient algorithm
*
* @param prob acceptance probability at current update
*/
void rescale(double prob);
/**
* The RWMetropolis method keeps a running mean of the acceptance
* probabilities, which is updated every time the rescale function
* is called. The checkAdaptation function returns true if the logit
* of the running mean is within 0.50 of the target.
*/
bool checkAdaptation() const;
/**
* Modifies the given value vector in place by adding an
* independent normal increment to each element. It can be
* overridden to provide non-normal increments, or a random walk
* on some transformed scale (but see RMetropolis#logJacobian).
*
* Note that this function does not modify the value of the
* RWMetropolis object.
*
*/
virtual void step(std::vector<double> &value, double s, RNG *rng) const;
/**
* If the random walk takes place on a transformed scale
* (e.g. log, logistic), then the log density of the target
* distribution must be penalized by the log Jacobian of the
* transformation.
*
* This function calculates the log Jacobian at the given value.
* By default, the random walk takes place on the original scale
* and therefore the penalty is zero.
*/
virtual double logJacobian(std::vector<double> const &value) const;
/**
* Returns the log of the probability density function of the target
* distribution at the current value.
*/
virtual double logDensity() const = 0;
};
#endif /* RW_METROPOLIS_H_ */
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