/usr/include/JAGS/model/BUGSModel.h is in jags 4.2.0-2.
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 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 | #ifndef BUGS_MODEL_H_
#define BUGS_MODEL_H_
#include <vector>
#include <map>
#include <utility>
#include <string>
#include <model/Model.h>
#include <model/SymTab.h>
#include <model/MonitorInfo.h>
namespace jags {
/**
* @short Model with symbol table
*
* A BUGS model is a subclass of Model that contains a symbol table
* which is used to store certain nodes in arrays. The array format
* gives a convenient way of looking up nodes by name.
*/
class BUGSModel : public Model
{
SymTab _symtab;
//std::map<Node const*, std::pair<std::string, Range> > _node_map;
std::list<MonitorInfo> _bugs_monitors;
public:
BUGSModel(unsigned int nchain);
~BUGSModel();
/**
* Returns the symbol table of the BUGSModel.
*/
SymTab &symtab();
/**
* Writes out selected monitors in CODA format.
*
* @param nodes Vector of nodes to write out. Each node is
* described by a pair consisting of a name and a range of
* indices. If a node is not being monitored, then it is ignored.
*
* @param prefix String giving prefix to be prepened to the output
* file names.
*
* @param warn String that will contain any warning messages on
* exit. It is cleared on entry.
*
* @exception logic_error
*/
void coda(std::vector<std::pair<std::string,Range> > const &nodes,
std::string const &prefix, std::string &warn);
/**
* Write out all monitors in CODA format
*/
void coda(std::string const &prefix, std::string &warn);
/**
* Sets the state of the RNG, and the values of the unobserved
* stochastic nodes in the model, for a given chain.
*
* @param param_table STL map, in which each entry relates a
* variable name to an SArray. If the name is ".RNG.state" or
* ".RNG.seed", then the SArray is used to set the state of the RNG.
* Otherwise the SArray value is used to set the unobserved
* stochastic nodes in the model. Each SArray must have the same
* dimensions as the NodeArray in the symbol table with the
* corresponding name. Elements of the SArray must be set to the
* missing value, JAGS_NA, unless they correspond to an element of
* an unobserved StochasticNode.
*
* @param chain Number of chain (starting from zero) for which
* parameter values should be set.
*
* @see RNG#init RNG#setState
* @exception runtime_error
*/
void setParameters(std::map<std::string, SArray> const ¶m_table,
unsigned int chain);
/**
* Creates a new Monitor. The BUGSModel is responsible for the
* memory management of any monitor created this way. It is not
* possible to create two monitors with the same name, range and
* type.
*
* @param name Name of the node array
*
* @param range Subset of indices of the node array defining hte
* node to be monitored.
*
* @param thin Thinning interval for monitor
*
* @param type Type of monitor to create
*
* @param msg User-friendly error message that may be given if no
* monitor can be created.
*
* @return True if the monitor was created.
*/
bool setMonitor(std::string const &name, Range const &range,
unsigned int thin, std::string const &type,
std::string &msg);
/**
* Deletes a Monitor that has been previously created with a call
* to setMonitor.
*
* @return True if the monitor was deleted.
*/
bool deleteMonitor(std::string const &name, Range const &range,
std::string const &type);
/**
* Traverses the list of monitor factories requesting default
* monitors of the given type. The function returns true after the
* first monitor factory has added at least one node to the monitor
* list. If none of the available monitor factories can create
* default monitors of the given type, the return value is false.
*
* @see MonitorFactory#addDefaultMonitors
*/
bool setDefaultMonitors(std::string const &type, unsigned int thin);
/**
* Removes all Monitors of the given type.
*/
void clearMonitors(std::string const &type);
/**
* Writes the names of the samplers, and the corresponding
* sampled nodes vectors to the given vector.
*
* @param sampler_names vector that is modified during the call On
* exit it will contain an element for each Sampler in the model.
* Each element is a vector of strings: the first string is the
* name of the sampler, and the remaining strings are the names of
* the nodes sampled by that Sampler.
*/
void samplerNames(std::vector<std::vector<std::string> > &sampler_names)
const;
};
} /* namespace jags */
#endif /* BUGS_MODEL_H_ */
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