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

6 files changed, 0 insertions, 706 deletions

diff --git a/gi/clda/src/Makefile.am b/gi/clda/src/Makefile.am
deleted file mode 100644
index cdca1f97..00000000
--- a/gi/clda/src/Makefile.am
+++ /dev/null
@@ -1,6 +0,0 @@
-bin_PROGRAMS = clda
-
-clda_SOURCES = clda.cc
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare -funroll-loops -I$(top_srcdir)/utils $(GTEST_CPPFLAGS)
-AM_LDFLAGS = $(top_srcdir)/utils/libutils.a -lz
diff --git a/gi/clda/src/ccrp.h b/gi/clda/src/ccrp.h
deleted file mode 100644
index a7c2825c..00000000
--- a/gi/clda/src/ccrp.h
+++ /dev/null
@@ -1,291 +0,0 @@
-#ifndef _CCRP_H_
-#define _CCRP_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <vector>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-
-// Chinese restaurant process (Pitman-Yor parameters) with table tracking.
-
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP {
- public:
-  CCRP(double disc, double conc) :
-    num_tables_(),
-    num_customers_(),
-    discount_(disc),
-    concentration_(conc),
-    discount_prior_alpha_(std::numeric_limits<double>::quiet_NaN()),
-    discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-    concentration_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    concentration_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {}
-
-  CCRP(double d_alpha, double d_beta, double c_shape, double c_rate, double d = 0.1, double c = 10.0) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    concentration_(c),
-    discount_prior_alpha_(d_alpha),
-    discount_prior_beta_(d_beta),
-    concentration_prior_shape_(c_shape),
-    concentration_prior_rate_(c_rate) {}
-
-  double discount() const { return discount_; }
-  double concentration() const { return concentration_; }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_alpha_);
-  }
-
-  bool has_concentration_prior() const {
-    return !std::isnan(concentration_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_locs_.clear();
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->second.table_counts_.size();
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->total_dish_count_;
-  }
-
-  // returns +1 or 0 indicating whether a new table was opened
-  int increment(const Dish& dish, const double& p0, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    bool share_table = false;
-    if (loc.total_dish_count_) {
-      const double p_empty = (concentration_ + num_tables_ * discount_) * p0;
-      const double p_share = (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      share_table = rng->SelectSample(p_empty, p_share);
-    }
-    if (share_table) {
-      double r = rng->next() * (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= (*ti - discount_);
-        if (r <= 0.0) {
-          ++(*ti);
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-    } else {
-      loc.table_counts_.push_back(1u);
-      ++num_tables_;
-    }
-    ++loc.total_dish_count_;
-    ++num_customers_;
-    return (share_table ? 0 : 1);
-  }
-
-  // returns -1 or 0, indicating whether a table was closed
-  int decrement(const Dish& dish, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    assert(loc.total_dish_count_);
-    if (loc.total_dish_count_ == 1) {
-      dish_locs_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      return -1;
-    } else {
-      int delta = 0;
-      // sample customer to remove UNIFORMLY. that is, do NOT use the discount
-      // here. if you do, it will introduce (unwanted) bias!
-      double r = rng->next() * loc.total_dish_count_;
-      --loc.total_dish_count_;
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= *ti;
-        if (r <= 0.0) {
-          if ((--(*ti)) == 0) {
-            --num_tables_;
-            delta = -1;
-            loc.table_counts_.erase(ti);
-          }
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-      --num_customers_;
-      return delta;
-    }
-  }
-
-  double prob(const Dish& dish, const double& p0) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    const double r = num_tables_ * discount_ + concentration_;
-    if (it == dish_locs_.end()) {
-      return r * p0 / (num_customers_ + concentration_);
-    } else {
-      return (it->second.total_dish_count_ - discount_ * it->second.table_counts_.size() + r * p0) /
-               (num_customers_ + concentration_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, concentration_);
-  }
-
-  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& concentration) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = log_beta_density(discount, discount_prior_alpha_, discount_prior_beta_);
-    if (has_concentration_prior())
-      lp += log_gamma_density(concentration, concentration_prior_shape_, concentration_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        lp += lgamma(concentration) - lgamma(concentration + num_customers_)
-             + num_tables_ * log(discount) + lgamma(concentration / discount + num_tables_)
-             - lgamma(concentration / discount);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          for (std::list<unsigned>::const_iterator ti = cur.table_counts_.begin(); ti != cur.table_counts_.end(); ++ti) {
-            lp += lgamma(*ti - discount) - r;
-          }
-        }
-      } else {
-        assert(!"not implemented yet");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng) {
-    assert(has_discount_prior() || has_concentration_prior());
-    DiscountResampler dr(*this);
-    ConcentrationResampler cr(*this);
-    const int niterations = 10;
-    double gamma_upper = std::numeric_limits<double>::infinity();
-    for (int iter = 0; iter < 5; ++iter) {
-      if (has_concentration_prior()) {
-        concentration_ = slice_sampler1d(cr, concentration_, *rng, 0.0,
-                               gamma_upper, 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);
-      }
-    }
-    concentration_ = slice_sampler1d(cr, concentration_, *rng, 0.0,
-                             gamma_upper, 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_discount) const {
-      return crp_.log_crp_prob(proposed_discount, crp_.concentration_);
-    }
-  };
-
-  struct ConcentrationResampler {
-    ConcentrationResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_concentration) const {
-      return crp_.log_crp_prob(crp_.discount_, proposed_concentration);
-    }
-  };
-
-  struct DishLocations {
-    DishLocations() : total_dish_count_() {}
-    unsigned total_dish_count_;        // customers at all tables with this dish
-    std::list<unsigned> table_counts_; // list<> gives O(1) deletion and insertion, which we want
-                                       // .size() is the number of tables for this dish
-  };
-
-  void Print(std::ostream* out) const {
-    for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-         it != dish_locs_.end(); ++it) {
-      (*out) << it->first << " (" << it->second.total_dish_count_ << " on " << it->second.table_counts_.size() << " tables): ";
-      for (typename std::list<unsigned>::const_iterator i = it->second.table_counts_.begin();
-           i != it->second.table_counts_.end(); ++i) {
-        (*out) << " " << *i;
-      }
-      (*out) << std::endl;
-    }
-  }
-
-  typedef typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_locs_.begin();
-  }
-  const_iterator end() const {
-    return dish_locs_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  std::tr1::unordered_map<Dish, DishLocations, DishHash> dish_locs_;
-
-  double discount_;
-  double concentration_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_alpha_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on concentration_ (NaN if no prior)
-  double concentration_prior_shape_;
-  double concentration_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif
diff --git a/gi/clda/src/clda.cc b/gi/clda/src/clda.cc
deleted file mode 100644
index f548997f..00000000
--- a/gi/clda/src/clda.cc
+++ /dev/null
@@ -1,148 +0,0 @@
-#include <iostream>
-#include <vector>
-#include <map>
-#include <string>
-
-#include "timer.h"
-#include "crp.h"
-#include "ccrp.h"
-#include "sampler.h"
-#include "tdict.h"
-const size_t MAX_DOC_LEN_CHARS = 10000000;
-
-using namespace std;
-
-void ShowTopWordsForTopic(const map<WordID, int>& counts) {
-  multimap<int, WordID> ms;
-  for (map<WordID,int>::const_iterator it = counts.begin(); it != counts.end(); ++it)
-    ms.insert(make_pair(it->second, it->first));
-  int cc = 0;
-  for (multimap<int, WordID>::reverse_iterator it = ms.rbegin(); it != ms.rend(); ++it) {
-    cerr << it->first << ':' << TD::Convert(it->second) << " ";
-    ++cc;
-    if (cc==20) break;
-  }
-  cerr << endl;
-}
-
-int main(int argc, char** argv) {
-  if (argc != 3) {
-    cerr << "Usage: " << argv[0] << " num-classes num-samples\n";
-    return 1;
-  }
-  const int num_classes = atoi(argv[1]);
-  const int num_iterations = atoi(argv[2]);
-  const int burnin_size = num_iterations * 0.9;
-  if (num_classes < 2) {
-    cerr << "Must request more than 1 class\n";
-    return 1;
-  }
-  if (num_iterations < 5) {
-    cerr << "Must request more than 5 iterations\n";
-    return 1;
-  }
-  cerr << "CLASSES: " << num_classes << endl;
-  char* buf = new char[MAX_DOC_LEN_CHARS];
-  vector<vector<int> > wji;   // w[j][i] - observed word i of doc j
-  vector<vector<int> > zji;   // z[j][i] - topic assignment for word i of doc j
-  cerr << "READING DOCUMENTS\n";
-  while(cin) {
-    cin.getline(buf, MAX_DOC_LEN_CHARS);
-    if (buf[0] == 0) continue;
-    wji.push_back(vector<WordID>());
-    TD::ConvertSentence(buf, &wji.back());
-  }
-  cerr << "READ " << wji.size() << " DOCUMENTS\n";
-  MT19937 rng;
-  cerr << "INITIALIZING RANDOM TOPIC ASSIGNMENTS\n";
-  zji.resize(wji.size());
-  double disc = 0.1;
-  double beta = 10.0;
-  double alpha = 50.0;
-  const double uniform_topic = 1.0 / num_classes;
-  const double uniform_word = 1.0 / TD::NumWords();
-  vector<CCRP<int> > dr(zji.size(), CCRP<int>(1,1,1,1,disc, beta)); // dr[i] describes the probability of using a topic in document i
-  vector<CCRP<int> > wr(num_classes, CCRP<int>(1,1,1,1,disc, alpha)); // wr[k] describes the probability of generating a word in topic k
-  for (int j = 0; j < zji.size(); ++j) {
-    const size_t num_words = wji[j].size();
-    vector<int>& zj = zji[j];
-    const vector<int>& wj = wji[j];
-    zj.resize(num_words);
-    for (int i = 0; i < num_words; ++i) {
-      int random_topic = rng.next() * num_classes;
-      if (random_topic == num_classes) { --random_topic; }
-      zj[i] = random_topic;
-      const int word = wj[i];
-      dr[j].increment(random_topic, uniform_topic, &rng);
-      wr[random_topic].increment(word, uniform_word, &rng);
-    }
-  }
-  cerr << "SAMPLING\n";
-  vector<map<WordID, int> > t2w(num_classes);
-  Timer timer;
-  SampleSet<double> ss;
-  ss.resize(num_classes);
-  double total_time = 0;
-  for (int iter = 0; iter < num_iterations; ++iter) {
-    cerr << '.';
-    if (iter && iter % 10 == 0) {
-      total_time += timer.Elapsed();
-      timer.Reset();
-      double llh = 0;
-#if 1
-      for (int j = 0; j < dr.size(); ++j)
-        dr[j].resample_hyperparameters(&rng);
-      for (int j = 0; j < wr.size(); ++j)
-        wr[j].resample_hyperparameters(&rng);
-#endif
-
-      for (int j = 0; j < dr.size(); ++j)
-        llh += dr[j].log_crp_prob();
-      for (int j = 0; j < wr.size(); ++j)
-        llh += wr[j].log_crp_prob();
-      cerr << " [LLH=" << llh << " I=" << iter << "]\n";
-    }
-    for (int j = 0; j < zji.size(); ++j) {
-      const size_t num_words = wji[j].size();
-      vector<int>& zj = zji[j];
-      const vector<int>& wj = wji[j];
-      for (int i = 0; i < num_words; ++i) {
-        const int word = wj[i];
-        const int cur_topic = zj[i];
-        dr[j].decrement(cur_topic, &rng);
-        wr[cur_topic].decrement(word, &rng);
- 
-        for (int k = 0; k < num_classes; ++k) {
-          ss[k]= dr[j].prob(k, uniform_topic) * wr[k].prob(word, uniform_word);
-        }
-        const int new_topic = rng.SelectSample(ss);
-        dr[j].increment(new_topic, uniform_topic, &rng);
-        wr[new_topic].increment(word, uniform_word, &rng);
-        zj[i] = new_topic;
-        if (iter > burnin_size) {
-          ++t2w[cur_topic][word];
-        }
-      }
-    }
-  }
-  for (int i = 0; i < num_classes; ++i) {
-    cerr << "---------------------------------\n";
-    cerr << " final PYP(" << wr[i].discount() << "," << wr[i].concentration() << ")\n";
-    ShowTopWordsForTopic(t2w[i]);
-  }
-  cerr << "-------------\n";
-#if 0
-  for (int j = 0; j < zji.size(); ++j) {
-    const size_t num_words = wji[j].size();
-    vector<int>& zj = zji[j];
-    const vector<int>& wj = wji[j];
-    zj.resize(num_words);
-    for (int i = 0; i < num_words; ++i) {
-      cerr << TD::Convert(wji[j][i]) << '(' << zj[i] << ") ";
-    }
-    cerr << endl;
-  }
-#endif
-  return 0;
-}
-
diff --git a/gi/clda/src/crp.h b/gi/clda/src/crp.h
deleted file mode 100644
index 9d35857e..00000000
--- a/gi/clda/src/crp.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _CRP_H_
-#define _CRP_H_
-
-// shamelessly adapted from code by Phil Blunsom and Trevor Cohn
-
-#include <boost/functional/hash.hpp>
-#include <tr1/unordered_map>
-
-#include "prob.h"
-
-template <typename DishType, typename Hash = boost::hash<DishType> >
-class CRP {
- public:
-  CRP(double alpha) : alpha_(alpha), palpha_(alpha), total_customers_() {}
-  void increment(const DishType& dish);
-  void decrement(const DishType& dish);
-  void erase(const DishType& dish) {
-    counts_.erase(dish);
-  }
-  inline int count(const DishType& dish) const {
-    const typename MapType::const_iterator i = counts_.find(dish);
-    if (i == counts_.end()) return 0; else return i->second;
-  }
-  inline prob_t prob(const DishType& dish, const prob_t& p0) const {
-    return (prob_t(count(dish)) + palpha_ * p0) / prob_t(total_customers_ + alpha_);
-  }
- private:
-  typedef std::tr1::unordered_map<DishType, int, Hash> MapType;
-  MapType counts_;
-  const double alpha_;
-  const prob_t palpha_;
-  int total_customers_;
-};
-
-template <typename Dish, typename Hash>
-void CRP<Dish,Hash>::increment(const Dish& dish) {
-  ++counts_[dish];
-  ++total_customers_;
-}
-
-template <typename Dish, typename Hash>
-void CRP<Dish,Hash>::decrement(const Dish& dish) {
-  typename MapType::iterator i = counts_.find(dish);
-  assert(i != counts_.end());
-  if (--i->second == 0)
-    counts_.erase(i);
-  --total_customers_;
-}
-
-#endif
diff --git a/gi/clda/src/slice_sampler.h b/gi/clda/src/slice_sampler.h
deleted file mode 100644
index aa48a169..00000000
--- a/gi/clda/src/slice_sampler.h
+++ /dev/null
@@ -1,191 +0,0 @@
-//! slice-sampler.h is an MCMC slice sampler
-//!
-//! Mark Johnson, 1st August 2008
-
-#ifndef SLICE_SAMPLER_H
-#define SLICE_SAMPLER_H
-
-#include <algorithm>
-#include <cassert>
-#include <cmath>
-#include <iostream>
-#include <limits>
-
-//! slice_sampler_rfc_type{} returns the value of a user-specified
-//! function if the argument is within range, or - infinity otherwise
-//
-template <typename F, typename Fn, typename U>
-struct slice_sampler_rfc_type {
-  F min_x, max_x;
-  const Fn& f;
-  U max_nfeval, nfeval;
-  slice_sampler_rfc_type(F min_x, F max_x, const Fn& f, U max_nfeval) 
-    : min_x(min_x), max_x(max_x), f(f), max_nfeval(max_nfeval), nfeval(0) { }
-    
-  F operator() (F x) {
-    if (min_x < x && x < max_x) {
-      assert(++nfeval <= max_nfeval);
-      F fx = f(x);
-      assert(std::isfinite(fx));
-      return fx;
-    }
-      return -std::numeric_limits<F>::infinity();
-  }
-};  // slice_sampler_rfc_type{}
-
-//! slice_sampler1d() implements the univariate "range doubling" slice sampler
-//! described in Neal (2003) "Slice Sampling", The Annals of Statistics 31(3), 705-767.
-//
-template <typename F, typename LogF, typename Uniform01>
-F slice_sampler1d(const LogF& logF0,               //!< log of function to sample
-		  F x,                             //!< starting point
-		  Uniform01& u01,                  //!< uniform [0,1) random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,                       //!< guess at initial width
-		  unsigned nsamples=1,             //!< number of samples to draw
-		  unsigned max_nfeval=200)         //!< max number of function evaluations
-{
-  typedef unsigned U;
-  slice_sampler_rfc_type<F,LogF,U> logF(min_x, max_x, logF0, max_nfeval);
-
-  assert(std::isfinite(x));
-
-  if (w <= 0.0) {                           // set w to a default width 
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, (F) 0.1);
-  }
-  assert(std::isfinite(w));
-
-  F logFx = logF(x);
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F logY = logFx + log(u01()+1e-100);     //! slice logFx at this value
-    assert(std::isfinite(logY));
-
-    F xl = x - w*u01();                     //! lower bound on slice interval
-    F logFxl = logF(xl);
-    F xr = xl + w;                          //! upper bound on slice interval
-    F logFxr = logF(xr);
-
-    while (logY < logFxl || logY < logFxr)  // doubling procedure
-      if (u01() < 0.5) 
-	logFxl = logF(xl -= xr - xl);
-      else
-	logFxr = logF(xr += xr - xl);
-	
-    F xl1 = xl;
-    F xr1 = xr;
-    while (true) {                          // shrinking procedure
-      F x1 = xl1 + u01()*(xr1 - xl1);
-      if (logY < logF(x1)) {
-	F xl2 = xl;                         // acceptance procedure
-	F xr2 = xr; 
-	bool d = false;
-	while (xr2 - xl2 > 1.1*w) {
-	  F xm = (xl2 + xr2)/2;
-	  if ((x < xm && x1 >= xm) || (x >= xm && x1 < xm))
-	    d = true;
-	  if (x1 < xm)
-	    xr2 = xm;
-	  else
-	    xl2 = xm;
-	  if (d && logY >= logF(xl2) && logY >= logF(xr2))
-	    goto unacceptable;
-	}
-	x = x1;
-	goto acceptable;
-      }
-      goto acceptable;
-    unacceptable:
-      if (x1 < x)                           // rest of shrinking procedure
-	xl1 = x1;
-      else 
-	xr1 = x1;
-    }
-  acceptable:
-    w = (4*w + (xr1 - xl1))/5;              // update width estimate
-  }
-  return x;
-}
-
-/*
-//! slice_sampler1d() implements a 1-d MCMC slice sampler.
-//! It should be correct for unimodal distributions, but
-//! not for multimodal ones.
-//
-template <typename F, typename LogP, typename Uniform01>
-F slice_sampler1d(const LogP& logP,     //!< log of distribution to sample
-		  F x,                  //!< initial sample
-		  Uniform01& u01,       //!< uniform random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,            //!< guess at initial width
-		  unsigned nsamples=1,  //!< number of samples to draw
-		  unsigned max_nfeval=200)  //!< max number of function evaluations
-{
-  typedef unsigned U;
-  assert(std::isfinite(x));
-  if (w <= 0.0) {
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, 0.1);
-  }
-  // TRACE4(x, min_x, max_x, w);
-  F logPx = logP(x);
-  assert(std::isfinite(logPx));
-  U nfeval = 1;
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F x0 = x;
-    F logU = logPx + log(u01()+1e-100);
-    assert(std::isfinite(logU));
-    F r = u01();
-    F xl = std::max(min_x, x - r*w);
-    F xr = std::min(max_x, x + (1-r)*w);
-    // TRACE3(x, logPx, logU);
-    while (xl > min_x && logP(xl) > logU) {
-      xl -= w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xl = std::max(xl, min_x);
-    while (xr < max_x && logP(xr) > logU) {
-      xr += w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xr = " << xr << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xr = std::min(xr, max_x);
-    while (true) {
-      r = u01();
-      x = r*xl + (1-r)*xr;
-      assert(std::isfinite(x));
-      logPx = logP(x);
-      // TRACE4(logPx, x, xl, xr);
-      assert(std::isfinite(logPx));
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << ", xr = " << xr << ", x = " << x << std::endl;
-      assert(nfeval < max_nfeval);
-      if (logPx > logU)
-        break;
-      else if (x > x0)
-          xr = x;
-        else
-          xl = x;
-    }
-    // w = (4*w + (xr-xl))/5;   // gradually adjust w
-  }
-  // TRACE2(logPx, x);
-  return x;
-}  // slice_sampler1d()
-*/
-
-#endif  // SLICE_SAMPLER_H
diff --git a/gi/clda/src/timer.h b/gi/clda/src/timer.h
deleted file mode 100644
index 123d9a94..00000000
--- a/gi/clda/src/timer.h
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef _TIMER_STATS_H_
-#define _TIMER_STATS_H_
-
-#include <ctime>
-
-struct Timer {
-  Timer() { Reset(); }
-  void Reset() {
-    start_t = clock();
-  }
-  double Elapsed() const {
-    const clock_t end_t = clock();
-    const double elapsed = (end_t - start_t) / 1000000.0;
-    return elapsed;
-  }
- private:
-  std::clock_t start_t;
-};
-
-#endif