Merge remote branch 'upstream/master'

Conflicts:
	Jamroot
	bjam
	decoder/Jamfile
	decoder/cdec.cc
	dpmert/Jamfile
	jam-files/sanity.jam
	klm/lm/Jamfile
	klm/util/Jamfile
	mira/Jamfile

1 files changed, 0 insertions, 253 deletions

diff --git a/utils/ccrp_onetable.h b/utils/ccrp_onetable.h
deleted file mode 100644
index abe399ea..00000000
--- a/utils/ccrp_onetable.h
+++ /dev/null
@@ -1,253 +0,0 @@
-#ifndef _CCRP_ONETABLE_H_
-#define _CCRP_ONETABLE_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-
-// Chinese restaurant process (Pitman-Yor parameters) with one table approximation
-
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP_OneTable {
-  typedef std::tr1::unordered_map<Dish, unsigned, DishHash> DishMapType;
- public:
-  CCRP_OneTable(double disc, double conc) :
-    num_tables_(),
-    num_customers_(),
-    discount_(disc),
-    alpha_(conc),
-    discount_prior_alpha_(std::numeric_limits<double>::quiet_NaN()),
-    discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-    alpha_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    alpha_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {}
-
-  CCRP_OneTable(double d_alpha, double d_beta, double c_shape, double c_rate, double d = 0.9, double c = 1.0) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    alpha_(c),
-    discount_prior_alpha_(d_alpha),
-    discount_prior_beta_(d_beta),
-    alpha_prior_shape_(c_shape),
-    alpha_prior_rate_(c_rate) {}
-
-  double discount() const { return discount_; }
-  double alpha() const { return alpha_; }
-  void set_alpha(double c) { alpha_ = c; }
-  void set_discount(double d) { discount_ = d; }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_alpha_);
-  }
-
-  bool has_alpha_prior() const {
-    return !std::isnan(alpha_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_counts_.clear();
-  }
-
-  unsigned num_tables() const {
-    return num_tables_;
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    if (it == dish_counts_.end()) return 0;
-    return 1;
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    if (it == dish_counts_.end()) return 0;
-    return it->second;
-  }
-
-  // returns +1 or 0 indicating whether a new table was opened
-  int increment(const Dish& dish) {
-    unsigned& dc = dish_counts_[dish];
-    ++dc;
-    ++num_customers_;
-    if (dc == 1) {
-      ++num_tables_;
-      return 1;
-    } else {
-      return 0;
-    }
-  }
-
-  // returns -1 or 0, indicating whether a table was closed
-  int decrement(const Dish& dish) {
-    unsigned& dc = dish_counts_[dish];
-    assert(dc > 0);
-    if (dc == 1) {
-      dish_counts_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      return -1;
-    } else {
-      assert(dc > 1);
-      --dc;
-      --num_customers_;
-      return 0;
-    }
-  }
-
-  double prob(const Dish& dish, const double& p0) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    const double r = num_tables_ * discount_ + alpha_;
-    if (it == dish_counts_.end()) {
-      return r * p0 / (num_customers_ + alpha_);
-    } else {
-      return (it->second - discount_ + r * p0) /
-               (num_customers_ + alpha_);
-    }
-  }
-
-  template <typename T>
-  T probT(const Dish& dish, const T& p0) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    const T r(num_tables_ * discount_ + alpha_);
-    if (it == dish_counts_.end()) {
-      return r * p0 / T(num_customers_ + alpha_);
-    } else {
-      return (T(it->second - discount_) + r * p0) /
-               T(num_customers_ + alpha_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, alpha_);
-  }
-
-  static double log_beta_density(const double& x, const double& alpha, const double& beta) {
-    assert(x > 0.0);
-    assert(x < 1.0);
-    assert(alpha > 0.0);
-    assert(beta > 0.0);
-    const double lp = (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
-    return lp;
-  }
-
-  static double log_gamma_density(const double& x, const double& shape, const double& rate) {
-    assert(x >= 0.0);
-    assert(shape > 0.0);
-    assert(rate > 0.0);
-    const double lp = (shape-1)*log(x) - shape*log(rate) - x/rate - lgamma(shape);
-    return lp;
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include P_0's
-  double log_crp_prob(const double& discount, const double& alpha) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = log_beta_density(discount, discount_prior_alpha_, discount_prior_beta_);
-    if (has_alpha_prior())
-      lp += log_gamma_density(alpha, alpha_prior_shape_, alpha_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        lp += lgamma(alpha) - lgamma(alpha + num_customers_)
-             + num_tables_ * log(discount) + lgamma(alpha / discount + num_tables_)
-             - lgamma(alpha / discount);
-        assert(std::isfinite(lp));
-        for (typename DishMapType::const_iterator it = dish_counts_.begin();
-             it != dish_counts_.end(); ++it) {
-          const unsigned& cur = it->second;
-          lp += lgamma(cur - discount) - r;
-        }
-      } else {
-        assert(!"not implemented yet");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    assert(has_discount_prior() || has_alpha_prior());
-    DiscountResampler dr(*this);
-    ConcentrationResampler cr(*this);
-    for (unsigned iter = 0; iter < nloop; ++iter) {
-      if (has_alpha_prior()) {
-        alpha_ = slice_sampler1d(cr, alpha_, *rng, 0.0,
-                               std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      }
-      if (has_discount_prior()) {
-        discount_ = slice_sampler1d(dr, discount_, *rng, std::numeric_limits<double>::min(),
-                               1.0, 0.0, niterations, 100*niterations);
-      }
-    }
-    alpha_ = slice_sampler1d(cr, alpha_, *rng, 0.0,
-                             std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const CCRP_OneTable& crp) : crp_(crp) {}
-    const CCRP_OneTable& crp_;
-    double operator()(const double& proposed_discount) const {
-      return crp_.log_crp_prob(proposed_discount, crp_.alpha_);
-    }
-  };
-
-  struct ConcentrationResampler {
-    ConcentrationResampler(const CCRP_OneTable& crp) : crp_(crp) {}
-    const CCRP_OneTable& crp_;
-    double operator()(const double& proposed_alpha) const {
-      return crp_.log_crp_prob(crp_.discount_, proposed_alpha);
-    }
-  };
-
-  void Print(std::ostream* out) const {
-    (*out) << "PYP(d=" << discount_ << ",c=" << alpha_ << ") customers=" << num_customers_ << std::endl;
-    for (typename DishMapType::const_iterator it = dish_counts_.begin(); it != dish_counts_.end(); ++it) {
-      (*out) << "  " << it->first << " = " << it->second << std::endl;
-    }
-  }
-
-  typedef typename DishMapType::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_counts_.begin();
-  }
-  const_iterator end() const {
-    return dish_counts_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  DishMapType dish_counts_;
-
-  double discount_;
-  double alpha_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_alpha_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on alpha_ (NaN if no prior)
-  double alpha_prior_shape_;
-  double alpha_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP_OneTable<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif