sequenzo 0.1.24__cp311-cp311-macosx_10_9_x86_64.whl

sequenzo/clustering/sequenzo_fastcluster/src/fastcluster.cpp

@@ -0,0 +1,1877 @@
+/*
+  fastcluster: Fast hierarchical clustering routines for R and Python
+
+  Copyright:
+    * Until package version 1.1.23: © 2011 Daniel Müllner <https://danifold.net>
+    * All changes from version 1.1.24 on: © Google Inc. <https://www.google.com>
+
+  This library implements various fast algorithms for hierarchical,
+  agglomerative clustering methods:
+
+  (1) Algorithms for the "stored matrix approach": the input is the array of
+      pairwise dissimilarities.
+
+      MST_linkage_core: single linkage clustering with the "minimum spanning
+      tree algorithm (Rohlfs)
+
+      NN_chain_core: nearest-neighbor-chain algorithm, suitable for single,
+      complete, average, weighted and Ward linkage (Murtagh)
+
+      generic_linkage: generic algorithm, suitable for all distance update
+      formulas (Müllner)
+
+  (2) Algorithms for the "stored data approach": the input are points in a
+      vector space.
+
+      MST_linkage_core_vector: single linkage clustering for vector data
+
+      generic_linkage_vector: generic algorithm for vector data, suitable for
+      the Ward, centroid and median methods.
+
+      generic_linkage_vector_alternative: alternative scheme for updating the
+      nearest neighbors. This method seems faster than "generic_linkage_vector"
+      for the centroid and median methods but slower for the Ward method.
+
+  All these implementation treat infinity values correctly. They throw an
+  exception if a NaN distance value occurs.
+*/
+
+// Older versions of Microsoft Visual Studio do not have the fenv header.
+#ifdef _MSC_VER
+#if (_MSC_VER == 1500 || _MSC_VER == 1600)
+#define NO_INCLUDE_FENV
+#endif
+#endif
+// NaN detection via fenv might not work on systems with software
+// floating-point emulation (bug report for Debian armel).
+#ifdef __SOFTFP__
+#define NO_INCLUDE_FENV
+#endif
+#ifdef NO_INCLUDE_FENV
+#pragma message("Do not use fenv header.")
+#else
+#pragma message("Use fenv header.")
+/* The following #pragma is necessary even if it generates a warning in many
+   compilers. Quoting https://en.cppreference.com/w/cpp/numeric/fenv:
+   "The floating-point environment access and modification is only meaningful
+   when #pragma STDC FENV_ACCESS is supported and is set to ON. [...]
+   In practice, few current compilers, such as HP aCC, Oracle Studio, or IBM XL,
+   support the #pragma explicitly, but most compilers allow meaningful access
+   to the floating-point environment anyway."
+*/
+#pragma STDC FENV_ACCESS ON
+#pragma messag("If there is a warning about unknown #pragma STDC FENV_ACCESS, this can be ignored.")
+#include <fenv.h>
+#endif
+
+#include <cmath> // for std::pow, std::sqrt
+#include <cstddef> // for std::ptrdiff_t
+#include <limits> // for std::numeric_limits<...>::infinity()
+#include <algorithm> // for std::fill_n
+#include <stdexcept> // for std::runtime_error
+#include <string> // for std::string
+
+#include <cfloat> // also for DBL_MAX, DBL_MIN
+#ifndef DBL_MANT_DIG
+#error The constant DBL_MANT_DIG could not be defined.
+#endif
+#define T_FLOAT_MANT_DIG DBL_MANT_DIG
+
+#ifndef LONG_MAX
+#include <climits>
+#endif
+#ifndef LONG_MAX
+#error The constant LONG_MAX could not be defined.
+#endif
+#ifndef INT_MAX
+#error The constant INT_MAX could not be defined.
+#endif
+
+#ifndef INT32_MAX
+#ifdef _MSC_VER
+#if _MSC_VER >= 1600
+#define __STDC_LIMIT_MACROS
+#include <stdint.h>
+#else
+typedef __int32 int_fast32_t;
+typedef __int64 int64_t;
+#endif
+#else
+#define __STDC_LIMIT_MACROS
+#include <stdint.h>
+#endif
+#endif
+
+#define FILL_N std::fill_n
+#ifdef _MSC_VER
+#if _MSC_VER < 1600
+#undef FILL_N
+#define FILL_N stdext::unchecked_fill_n
+#endif
+#endif
+
+// Suppress warnings about (potentially) uninitialized variables.
+#ifdef _MSC_VER
+	#pragma warning (disable:4700)
+#endif
+
+#ifndef HAVE_DIAGNOSTIC
+#if __GNUC__ > 4 || (__GNUC__ == 4 && (__GNUC_MINOR__ >= 6))
+#define HAVE_DIAGNOSTIC 1
+#endif
+#endif
+
+#ifndef HAVE_VISIBILITY
+#if __GNUC__ >= 4
+#define HAVE_VISIBILITY 1
+#endif
+#endif
+
+/* Since the public interface is given by the Python respectively R interface,
+ * we do not want other symbols than the interface initalization routines to be
+ * visible in the shared object file. The "visibility" switch is a GCC concept.
+ * Hiding symbols keeps the relocation table small and decreases startup time.
+ * See http://gcc.gnu.org/wiki/Visibility
+ */
+#if HAVE_VISIBILITY
+#pragma GCC visibility push(hidden)
+#endif
+
+typedef int_fast32_t t_index;
+#ifndef INT32_MAX
+#define MAX_INDEX 0x7fffffffL
+#else
+#define MAX_INDEX INT32_MAX
+#endif
+#if (LONG_MAX < MAX_INDEX)
+#error The integer format "t_index" must not have a greater range than "long int".
+#endif
+#if (INT_MAX > MAX_INDEX)
+#error The integer format "int" must not have a greater range than "t_index".
+#endif
+typedef double t_float;
+
+/* Method codes.
+
+   These codes must agree with the METHODS array in fastcluster.R and the
+   dictionary mthidx in fastcluster.py.
+*/
+enum method_codes {
+  // non-Euclidean methods
+  METHOD_METR_SINGLE           = 0,
+  METHOD_METR_COMPLETE         = 1,
+  METHOD_METR_AVERAGE          = 2,
+  METHOD_METR_WEIGHTED         = 3,
+  METHOD_METR_WARD             = 4,
+  METHOD_METR_WARD_D           = METHOD_METR_WARD,
+  METHOD_METR_CENTROID         = 5,
+  METHOD_METR_MEDIAN           = 6,
+  METHOD_METR_WARD_D2          = 7,
+
+  MIN_METHOD_CODE              = 0,
+  MAX_METHOD_CODE              = 7
+};
+
+enum method_codes_vector {
+  // Euclidean methods
+  METHOD_VECTOR_SINGLE         = 0,
+  METHOD_VECTOR_WARD           = 1,
+  METHOD_VECTOR_WARD_D2        = 4,
+  METHOD_VECTOR_CENTROID       = 2,
+  METHOD_VECTOR_MEDIAN         = 3,
+
+  MIN_METHOD_VECTOR_CODE       = 0,
+  MAX_METHOD_VECTOR_CODE       = 3
+};
+
+// self-destructing array pointer
+template <typename type>
+class auto_array_ptr{
+private:
+  type * ptr;
+  auto_array_ptr(auto_array_ptr const &); // non construction-copyable
+  auto_array_ptr& operator=(auto_array_ptr const &); // non copyable
+public:
+  auto_array_ptr()
+    : ptr(NULL)
+  { }
+  template <typename index>
+  auto_array_ptr(index const size)
+    : ptr(new type[size])
+  { }
+  template <typename index, typename value>
+  auto_array_ptr(index const size, value const val)
+    : ptr(new type[size])
+  {
+    FILL_N(ptr, size, val);
+  }
+  ~auto_array_ptr() {
+    delete [] ptr; }
+  void free() {
+    delete [] ptr;
+    ptr = NULL;
+  }
+  template <typename index>
+  void init(index const size) {
+    ptr = new type [size];
+  }
+  template <typename index, typename value>
+  void init(index const size, value const val) {
+    init(size);
+    FILL_N(ptr, size, val);
+  }
+  inline operator type *() const { return ptr; }
+};
+
+struct node {
+  t_index node1, node2;
+  t_float dist;
+};
+
+inline bool operator< (const node a, const node b) {
+  return (a.dist < b.dist);
+}
+
+class cluster_result {
+private:
+  auto_array_ptr<node> Z;
+  t_index pos;
+
+public:
+  cluster_result(const t_index size)
+    : Z(size)
+    , pos(0)
+  {}
+
+  void append(const t_index node1, const t_index node2, const t_float dist) {
+    Z[pos].node1 = node1;
+    Z[pos].node2 = node2;
+    Z[pos].dist  = dist;
+    ++pos;
+  }
+
+  node * operator[] (const t_index idx) const { return Z + idx; }
+
+  /* Define several methods to postprocess the distances. All these functions
+     are monotone, so they do not change the sorted order of distances. */
+
+  void sqrt() const {
+    for (node * ZZ=Z; ZZ!=Z+pos; ++ZZ) {
+      ZZ->dist = std::sqrt(ZZ->dist);
+    }
+  }
+
+  void sqrt(const t_float) const { // ignore the argument
+    sqrt();
+  }
+
+  void sqrtdouble(const t_float) const { // ignore the argument
+    for (node * ZZ=Z; ZZ!=Z+pos; ++ZZ) {
+      ZZ->dist = std::sqrt(2*ZZ->dist);
+    }
+  }
+
+  void sqrtward(const t_float) const { // ignore the argument
+    for (node * ZZ=Z; ZZ!=Z+pos; ++ZZ) {
+      ZZ->dist = 2*ZZ->dist;
+    }
+  }
+
+  #ifdef R_pow
+  #define my_pow R_pow
+  #else
+  #define my_pow std::pow
+  #endif
+
+  void power(const t_float p) const {
+    t_float const q = 1/p;
+    for (node * ZZ=Z; ZZ!=Z+pos; ++ZZ) {
+      ZZ->dist = my_pow(ZZ->dist,q);
+    }
+  }
+
+  void plusone(const t_float) const { // ignore the argument
+    for (node * ZZ=Z; ZZ!=Z+pos; ++ZZ) {
+      ZZ->dist += 1;
+    }
+  }
+
+  void divide(const t_float denom) const {
+    for (node * ZZ=Z; ZZ!=Z+pos; ++ZZ) {
+      ZZ->dist /= denom;
+    }
+  }
+};
+
+class doubly_linked_list {
+  /*
+    Class for a doubly linked list. Initially, the list is the integer range
+    [0, size]. We provide a forward iterator and a method to delete an index
+    from the list.
+
+    Typical use: for (i=L.start; L<size; i=L.succ[I])
+    or
+    for (i=somevalue; L<size; i=L.succ[I])
+  */
+public:
+  t_index start;
+  auto_array_ptr<t_index> succ;
+
+private:
+  auto_array_ptr<t_index> pred;
+  // Not necessarily private, we just do not need it in this instance.
+
+public:
+  doubly_linked_list(const t_index size)
+    // Initialize to the given size.
+    : start(0)
+    , succ(size+1)
+    , pred(size+1)
+  {
+    for (t_index i=0; i<size; ++i) {
+      pred[i+1] = i;
+      succ[i] = i+1;
+    }
+    // pred[0] is never accessed!
+    //succ[size] is never accessed!
+  }
+
+  ~doubly_linked_list() {}
+
+  void remove(const t_index idx) {
+    // Remove an index from the list.
+    if (idx==start) {
+      start = succ[idx];
+    }
+    else {
+      succ[pred[idx]] = succ[idx];
+      pred[succ[idx]] = pred[idx];
+    }
+    succ[idx] = 0; // Mark as inactive
+  }
+
+  bool is_inactive(t_index idx) const {
+    return (succ[idx]==0);
+  }
+};
+
+// Indexing functions
+// D is the upper triangular part of a symmetric (NxN)-matrix
+// We require r_ < c_ !
+#define D_(r_,c_) ( D[(static_cast<std::ptrdiff_t>(2*N-3-(r_))*(r_)>>1)+(c_)-1] )
+// Z is an ((N-1)x4)-array
+#define Z_(_r, _c) (Z[(_r)*4 + (_c)])
+
+/*
+  Lookup function for a union-find data structure.
+
+  The function finds the root of idx by going iteratively through all
+  parent elements until a root is found. An element i is a root if
+  nodes[i] is zero. To make subsequent searches faster, the entry for
+  idx and all its parents is updated with the root element.
+ */
+class union_find {
+private:
+  auto_array_ptr<t_index> parent;
+  t_index nextparent;
+
+public:
+  union_find(const t_index size)
+    : parent(size>0 ? 2*size-1 : 0, 0)
+    , nextparent(size)
+  { }
+
+  t_index Find (t_index idx) const {
+    if (parent[idx] != 0 ) { // a → b
+      t_index p = idx;
+      idx = parent[idx];
+      if (parent[idx] != 0 ) { // a → b → c
+        do {
+          idx = parent[idx];
+        } while (parent[idx] != 0);
+        do {
+          t_index tmp = parent[p];
+          parent[p] = idx;
+          p = tmp;
+        } while (parent[p] != idx);
+      }
+    }
+    return idx;
+  }
+
+  void Union (const t_index node1, const t_index node2) {
+    parent[node1] = parent[node2] = nextparent++;
+  }
+};
+
+class nan_error{};
+#ifdef FE_INVALID
+class fenv_error{};
+#endif
+
+static void MST_linkage_core(const t_index N, const t_float * const D,
+                             cluster_result & Z2) {
+/*
+    N: integer, number of data points
+    D: condensed distance matrix N*(N-1)/2
+    Z2: output data structure
+
+    The basis of this algorithm is an algorithm by Rohlf:
+
+    F. James Rohlf, Hierarchical clustering using the minimum spanning tree,
+    The Computer Journal, vol. 16, 1973, p. 93–95.
+*/
+  t_index i;
+  t_index idx2;
+  doubly_linked_list active_nodes(N);
+  auto_array_ptr<t_float> d(N);
+
+  t_index prev_node;
+  t_float min;
+
+  // first iteration
+  idx2 = 1;
+  min = std::numeric_limits<t_float>::infinity();
+  for (i=1; i<N; ++i) {
+    d[i] = D[i-1];
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+    if (d[i] < min) {
+      min = d[i];
+      idx2 = i;
+    }
+    else if (fc_isnan(d[i]))
+      throw (nan_error());
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  }
+  Z2.append(0, idx2, min);
+
+  for (t_index j=1; j<N-1; ++j) {
+    prev_node = idx2;
+    active_nodes.remove(prev_node);
+
+    idx2 = active_nodes.succ[0];
+    min = d[idx2];
+    for (i=idx2; i<prev_node; i=active_nodes.succ[i]) {
+      t_float tmp = D_(i, prev_node);
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+      if (tmp < d[i])
+        d[i] = tmp;
+      else if (fc_isnan(tmp))
+        throw (nan_error());
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+      if (d[i] < min) {
+        min = d[i];
+        idx2 = i;
+      }
+    }
+    for (; i<N; i=active_nodes.succ[i]) {
+      t_float tmp = D_(prev_node, i);
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+      if (d[i] > tmp)
+        d[i] = tmp;
+      else if (fc_isnan(tmp))
+        throw (nan_error());
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+      if (d[i] < min) {
+        min = d[i];
+        idx2 = i;
+      }
+    }
+    Z2.append(prev_node, idx2, min);
+  }
+}
+
+/* Functions for the update of the dissimilarity array */
+
+inline static void f_single( t_float * const b, const t_float a ) {
+  if (*b > a) *b = a;
+}
+inline static void f_complete( t_float * const b, const t_float a ) {
+  if (*b < a) *b = a;
+}
+inline static void f_average( t_float * const b, const t_float a, const t_float s, const t_float t) {
+  *b = s*a + t*(*b);
+  #ifndef FE_INVALID
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+  if (fc_isnan(*b)) {
+    throw(nan_error());
+  }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  #endif
+}
+inline static void f_weighted( t_float * const b, const t_float a) {
+  *b = (a+*b)*.5;
+  #ifndef FE_INVALID
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+  if (fc_isnan(*b)) {
+    throw(nan_error());
+  }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  #endif
+}
+inline static void f_ward( t_float * const b, const t_float a, const t_float c, const t_float s, const t_float t, const t_float v) {
+  *b = ( (v+s)*a - v*c + (v+t)*(*b) ) / (s+t+v);
+  //*b = a+(*b)-(t*a+s*(*b)+v*c)/(s+t+v);
+  #ifndef FE_INVALID
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+  if (fc_isnan(*b)) {
+    throw(nan_error());
+  }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  #endif
+}
+inline static void f_centroid( t_float * const b, const t_float a, const t_float stc, const t_float s, const t_float t) {
+  *b = s*a - stc + t*(*b);
+  #ifndef FE_INVALID
+  if (fc_isnan(*b)) {
+    throw(nan_error());
+  }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  #endif
+}
+inline static void f_median( t_float * const b, const t_float a, const t_float c_4) {
+  *b = (a+(*b))*.5 - c_4;
+  #ifndef FE_INVALID
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+  if (fc_isnan(*b)) {
+    throw(nan_error());
+  }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  #endif
+}
+
+template <method_codes method, typename t_members>
+static void NN_chain_core(const t_index N, t_float * const D, t_members * const members, cluster_result & Z2) {
+/*
+    N: integer
+    D: condensed distance matrix N*(N-1)/2
+    Z2: output data structure
+
+    This is the NN-chain algorithm, described on page 86 in the following book:
+
+    Fionn Murtagh, Multidimensional Clustering Algorithms,
+    Vienna, Würzburg: Physica-Verlag, 1985.
+*/
+  t_index i;
+
+  auto_array_ptr<t_index> NN_chain(N);
+  t_index NN_chain_tip = 0;
+
+  t_index idx1, idx2;
+
+  t_float size1, size2;
+  doubly_linked_list active_nodes(N);
+
+  t_float min;
+
+  for (t_float const * DD=D; DD!=D+(static_cast<std::ptrdiff_t>(N)*(N-1)>>1);
+       ++DD) {
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+    if (fc_isnan(*DD)) {
+      throw(nan_error());
+    }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  }
+
+  #ifdef FE_INVALID
+  if (feclearexcept(FE_INVALID)) throw fenv_error();
+  #endif
+
+  for (t_index j=0; j<N-1; ++j) {
+    if (NN_chain_tip <= 3) {
+      NN_chain[0] = idx1 = active_nodes.start;
+      NN_chain_tip = 1;
+
+      idx2 = active_nodes.succ[idx1];
+      min = D_(idx1,idx2);
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i]) {
+        if (D_(idx1,i) < min) {
+          min = D_(idx1,i);
+          idx2 = i;
+        }
+      }
+    }  // a: idx1   b: idx2
+    else {
+      NN_chain_tip -= 3;
+      idx1 = NN_chain[NN_chain_tip-1];
+      idx2 = NN_chain[NN_chain_tip];
+      min = idx1<idx2 ? D_(idx1,idx2) : D_(idx2,idx1);
+    }  // a: idx1   b: idx2
+
+    do {
+      NN_chain[NN_chain_tip] = idx2;
+
+      for (i=active_nodes.start; i<idx2; i=active_nodes.succ[i]) {
+        if (D_(i,idx2) < min) {
+          min = D_(i,idx2);
+          idx1 = i;
+        }
+      }
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i]) {
+        if (D_(idx2,i) < min) {
+          min = D_(idx2,i);
+          idx1 = i;
+        }
+      }
+
+      idx2 = idx1;
+      idx1 = NN_chain[NN_chain_tip++];
+
+    } while (idx2 != NN_chain[NN_chain_tip-2]);
+
+    Z2.append(idx1, idx2, min);
+
+    if (idx1>idx2) {
+      t_index tmp = idx1;
+      idx1 = idx2;
+      idx2 = tmp;
+    }
+
+    if (method==METHOD_METR_AVERAGE ||
+        method==METHOD_METR_WARD ||
+        method==METHOD_METR_WARD_D2) {
+      size1 = static_cast<t_float>(members[idx1]);
+      size2 = static_cast<t_float>(members[idx2]);
+      members[idx2] += members[idx1];
+    }
+
+    // Remove the smaller index from the valid indices (active_nodes).
+    active_nodes.remove(idx1);
+
+    switch (method) {
+    case METHOD_METR_SINGLE:
+      /*
+      Single linkage.
+
+      Characteristic: new distances are never longer than the old distances.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
+        f_single(&D_(i, idx2), D_(i, idx1) );
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; i<idx2; i=active_nodes.succ[i])
+        f_single(&D_(i, idx2), D_(idx1, i) );
+      // Update the distance matrix in the range (idx2, N).
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
+        f_single(&D_(idx2, i), D_(idx1, i) );
+      break;
+
+    case METHOD_METR_COMPLETE:
+      /*
+      Complete linkage.
+
+      Characteristic: new distances are never shorter than the old distances.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
+        f_complete(&D_(i, idx2), D_(i, idx1) );
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; i<idx2; i=active_nodes.succ[i])
+        f_complete(&D_(i, idx2), D_(idx1, i) );
+      // Update the distance matrix in the range (idx2, N).
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
+        f_complete(&D_(idx2, i), D_(idx1, i) );
+      break;
+
+    case METHOD_METR_AVERAGE: {
+      /*
+      Average linkage.
+
+      Shorter and longer distances can occur.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      t_float s = size1/(size1+size2);
+      t_float t = size2/(size1+size2);
+      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
+        f_average(&D_(i, idx2), D_(i, idx1), s, t );
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; i<idx2; i=active_nodes.succ[i])
+        f_average(&D_(i, idx2), D_(idx1, i), s, t );
+      // Update the distance matrix in the range (idx2, N).
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
+        f_average(&D_(idx2, i), D_(idx1, i), s, t );
+      break;
+    }
+
+    case METHOD_METR_WEIGHTED:
+      /*
+      Weighted linkage.
+
+      Shorter and longer distances can occur.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
+        f_weighted(&D_(i, idx2), D_(i, idx1) );
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; i<idx2; i=active_nodes.succ[i])
+        f_weighted(&D_(i, idx2), D_(idx1, i) );
+      // Update the distance matrix in the range (idx2, N).
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
+        f_weighted(&D_(idx2, i), D_(idx1, i) );
+      break;
+
+    case METHOD_METR_WARD:
+      /*
+      Ward linkage.
+
+      Shorter and longer distances can occur, not smaller than min(d1,d2)
+      but maybe bigger than max(d1,d2).
+      */
+      // Update the distance matrix in the range [start, idx1).
+      //t_float v = static_cast<t_float>(members[i]);
+      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
+        f_ward(&D_(i, idx2), D_(i, idx1), min,
+               size1, size2, static_cast<t_float>(members[i]) );
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; i<idx2; i=active_nodes.succ[i])
+        f_ward(&D_(i, idx2), D_(idx1, i), min,
+               size1, size2, static_cast<t_float>(members[i]) );
+      // Update the distance matrix in the range (idx2, N).
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
+        f_ward(&D_(idx2, i), D_(idx1, i), min,
+               size1, size2, static_cast<t_float>(members[i]) );
+      break;
+
+    case METHOD_METR_WARD_D2:
+      /*
+      Ward D2 linkage (with squared Euclidean distances).
+
+      Shorter and longer distances can occur, not smaller than min(d1,d2)
+      but maybe bigger than max(d1,d2).
+      Uses the same update formula as Ward, but with different post-processing.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
+        f_ward(&D_(i, idx2), D_(i, idx1), min,
+               size1, size2, static_cast<t_float>(members[i]) );
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; i<idx2; i=active_nodes.succ[i])
+        f_ward(&D_(i, idx2), D_(idx1, i), min,
+               size1, size2, static_cast<t_float>(members[i]) );
+      // Update the distance matrix in the range (idx2, N).
+      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
+        f_ward(&D_(idx2, i), D_(idx1, i), min,
+               size1, size2, static_cast<t_float>(members[i]) );
+      break;
+
+    default:
+      throw std::runtime_error(std::string("Invalid method."));
+    }
+  }
+  #ifdef FE_INVALID
+  if (fetestexcept(FE_INVALID)) throw fenv_error();
+  #endif
+}
+
+class binary_min_heap {
+  /*
+  Class for a binary min-heap. The data resides in an array A. The elements of
+  A are not changed but two lists I and R of indices are generated which point
+  to elements of A and backwards.
+
+  The heap tree structure is
+
+     H[2*i+1]     H[2*i+2]
+         \            /
+          \          /
+           ≤        ≤
+            \      /
+             \    /
+              H[i]
+
+  where the children must be less or equal than their parent. Thus, H[0]
+  contains the minimum. The lists I and R are made such that H[i] = A[I[i]]
+  and R[I[i]] = i.
+
+  This implementation is not designed to handle NaN values.
+  */
+private:
+  t_float * const A;
+  t_index size;
+  auto_array_ptr<t_index> I;
+  auto_array_ptr<t_index> R;
+
+  // no default constructor
+  binary_min_heap();
+  // noncopyable
+  binary_min_heap(binary_min_heap const &);
+  binary_min_heap & operator=(binary_min_heap const &);
+
+public:
+  binary_min_heap(t_float * const A_, const t_index size_)
+    : A(A_), size(size_), I(size), R(size)
+  { // Allocate memory and initialize the lists I and R to the identity. This
+    // does not make it a heap. Call heapify afterwards!
+    for (t_index i=0; i<size; ++i)
+      R[i] = I[i] = i;
+  }
+
+  binary_min_heap(t_float * const A_, const t_index size1, const t_index size2,
+                  const t_index start)
+    : A(A_), size(size1), I(size1), R(size2)
+  { // Allocate memory and initialize the lists I and R to the identity. This
+    // does not make it a heap. Call heapify afterwards!
+    for (t_index i=0; i<size; ++i) {
+      R[i+start] = i;
+      I[i] = i + start;
+    }
+  }
+
+  ~binary_min_heap() {}
+
+  void heapify() {
+    // Arrange the indices I and R so that H[i] := A[I[i]] satisfies the heap
+    // condition H[i] < H[2*i+1] and H[i] < H[2*i+2] for each i.
+    //
+    // Complexity: Θ(size)
+    // Reference: Cormen, Leiserson, Rivest, Stein, Introduction to Algorithms,
+    // 3rd ed., 2009, Section 6.3 “Building a heap”
+    t_index idx;
+    for (idx=(size>>1); idx>0; ) {
+      --idx;
+      update_geq_(idx);
+    }
+  }
+
+  inline t_index argmin() const {
+    // Return the minimal element.
+    return I[0];
+  }
+
+  void heap_pop() {
+    // Remove the minimal element from the heap.
+    --size;
+    I[0] = I[size];
+    R[I[0]] = 0;
+    update_geq_(0);
+  }
+
+  void remove(t_index idx) {
+    // Remove an element from the heap.
+    --size;
+    R[I[size]] = R[idx];
+    I[R[idx]] = I[size];
+    if ( H(size)<=A[idx] ) {
+      update_leq_(R[idx]);
+    }
+    else {
+      update_geq_(R[idx]);
+    }
+  }
+
+  void replace ( const t_index idxold, const t_index idxnew,
+                 const t_float val) {
+    R[idxnew] = R[idxold];
+    I[R[idxnew]] = idxnew;
+    if (val<=A[idxold])
+      update_leq(idxnew, val);
+    else
+      update_geq(idxnew, val);
+  }
+
+  void update ( const t_index idx, const t_float val ) const {
+    // Update the element A[i] with val and re-arrange the indices to preserve
+    // the heap condition.
+    if (val<=A[idx])
+      update_leq(idx, val);
+    else
+      update_geq(idx, val);
+  }
+
+  void update_leq ( const t_index idx, const t_float val ) const {
+    // Use this when the new value is not more than the old value.
+    A[idx] = val;
+    update_leq_(R[idx]);
+  }
+
+  void update_geq ( const t_index idx, const t_float val ) const {
+    // Use this when the new value is not less than the old value.
+    A[idx] = val;
+    update_geq_(R[idx]);
+  }
+
+private:
+  void update_leq_ (t_index i) const {
+    t_index j;
+    for ( ; (i>0) && ( H(i)<H(j=(i-1)>>1) ); i=j)
+      heap_swap(i,j);
+  }
+
+  void update_geq_ (t_index i) const {
+    t_index j;
+    for ( ; (j=2*i+1)<size; i=j) {
+      if ( H(j)>=H(i) ) {
+        ++j;
+        if ( j>=size || H(j)>=H(i) ) break;
+      }
+      else if ( j+1<size && H(j+1)<H(j) ) ++j;
+      heap_swap(i, j);
+    }
+  }
+
+  void heap_swap(const t_index i, const t_index j) const {
+    // Swap two indices.
+    t_index tmp = I[i];
+    I[i] = I[j];
+    I[j] = tmp;
+    R[I[i]] = i;
+    R[I[j]] = j;
+  }
+
+  inline t_float H(const t_index i) const {
+    return A[I[i]];
+  }
+
+};
+
+template <method_codes method, typename t_members>
+static void generic_linkage(const t_index N, t_float * const D, t_members * const members, cluster_result & Z2) {
+  /*
+    N: integer, number of data points
+    D: condensed distance matrix N*(N-1)/2
+    Z2: output data structure
+  */
+
+  const t_index N_1 = N-1;
+  t_index i, j; // loop variables
+  t_index idx1, idx2; // row and column indices
+
+  auto_array_ptr<t_index> n_nghbr(N_1); // array of nearest neighbors
+  auto_array_ptr<t_float> mindist(N_1); // distances to the nearest neighbors
+  auto_array_ptr<t_index> row_repr(N); // row_repr[i]: node number that the
+                                       // i-th row represents
+  doubly_linked_list active_nodes(N);
+  binary_min_heap nn_distances(&*mindist, N_1); // minimum heap structure for
+                        // the distance to the nearest neighbor of each point
+  t_index node1, node2; // node numbers in the output
+  t_float size1, size2; // and their cardinalities
+
+  t_float min; // minimum and row index for nearest-neighbor search
+  t_index idx;
+
+  for (i=0; i<N; ++i)
+    // Build a list of row ↔ node label assignments.
+    // Initially i ↦ i
+    row_repr[i] = i;
+
+  // Initialize the minimal distances:
+  // Find the nearest neighbor of each point.
+  // n_nghbr[i] = argmin_{j>i} D(i,j) for i in range(N-1)
+  t_float const * DD = D;
+  for (i=0; i<N_1; ++i) {
+    min = std::numeric_limits<t_float>::infinity();
+    for (idx=j=i+1; j<N; ++j, ++DD) {
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+      if (*DD<min) {
+        min = *DD;
+        idx = j;
+      }
+      else if (fc_isnan(*DD))
+        throw(nan_error());
+    }
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+    mindist[i] = min;
+    n_nghbr[i] = idx;
+  }
+
+  // Put the minimal distances into a heap structure to make the repeated
+  // global minimum searches fast.
+  nn_distances.heapify();
+
+  #ifdef FE_INVALID
+  if (feclearexcept(FE_INVALID)) throw fenv_error();
+  #endif
+
+  // Main loop: We have N-1 merging steps.
+  for (i=0; i<N_1; ++i) {
+    /*
+      Here is a special feature that allows fast bookkeeping and updates of the
+      minimal distances.
+
+      mindist[i] stores a lower bound on the minimum distance of the point i to
+      all points of higher index:
+
+          mindist[i] ≥ min_{j>i} D(i,j)
+
+      Normally, we have equality. However, this minimum may become invalid due
+      to the updates in the distance matrix. The rules are:
+
+      1) If mindist[i] is equal to D(i, n_nghbr[i]), this is the correct
+         minimum and n_nghbr[i] is a nearest neighbor.
+
+      2) If mindist[i] is smaller than D(i, n_nghbr[i]), this might not be the
+         correct minimum. The minimum needs to be recomputed.
+
+      3) mindist[i] is never bigger than the true minimum. Hence, we never
+         miss the true minimum if we take the smallest mindist entry,
+         re-compute the value if necessary (thus maybe increasing it) and
+         looking for the now smallest mindist entry until a valid minimal
+         entry is found. This step is done in the lines below.
+
+      The update process for D below takes care that these rules are
+      fulfilled. This makes sure that the minima in the rows D(i,i+1:)of D are
+      re-calculated when necessary but re-calculation is avoided whenever
+      possible.
+
+      The re-calculation of the minima makes the worst-case runtime of this
+      algorithm cubic in N. We avoid this whenever possible, and in most cases
+      the runtime appears to be quadratic.
+    */
+    idx1 = nn_distances.argmin();
+    if (method != METHOD_METR_SINGLE) {
+      while ( mindist[idx1] < D_(idx1, n_nghbr[idx1]) ) {
+        // Recompute the minimum mindist[idx1] and n_nghbr[idx1].
+        n_nghbr[idx1] = j = active_nodes.succ[idx1]; // exists, maximally N-1
+        min = D_(idx1,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          if (D_(idx1,j)<min) {
+            min = D_(idx1,j);
+            n_nghbr[idx1] = j;
+          }
+        }
+        /* Update the heap with the new true minimum and search for the
+           (possibly different) minimal entry. */
+        nn_distances.update_geq(idx1, min);
+        idx1 = nn_distances.argmin();
+      }
+    }
+
+    nn_distances.heap_pop(); // Remove the current minimum from the heap.
+    idx2 = n_nghbr[idx1];
+
+    // Write the newly found minimal pair of nodes to the output array.
+    node1 = row_repr[idx1];
+    node2 = row_repr[idx2];
+
+    if (method==METHOD_METR_AVERAGE ||
+        method==METHOD_METR_WARD ||
+        method==METHOD_METR_WARD_D2 ||
+        method==METHOD_METR_CENTROID) {
+      size1 = static_cast<t_float>(members[idx1]);
+      size2 = static_cast<t_float>(members[idx2]);
+      members[idx2] += members[idx1];
+    }
+    Z2.append(node1, node2, mindist[idx1]);
+
+    // Remove idx1 from the list of active indices (active_nodes).
+    active_nodes.remove(idx1);
+    // Index idx2 now represents the new (merged) node with label N+i.
+    row_repr[idx2] = N+i;
+
+    // Update the distance matrix
+    switch (method) {
+    case METHOD_METR_SINGLE:
+      /*
+        Single linkage.
+
+        Characteristic: new distances are never longer than the old distances.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_single(&D_(j, idx2), D_(j, idx1));
+        if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_single(&D_(j, idx2), D_(idx1, j));
+        // If the new value is below the old minimum in a row, update
+        // the mindist and n_nghbr arrays.
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      // Recompute the minimum mindist[idx2] and n_nghbr[idx2].
+      if (idx2<N_1) {
+        min = mindist[idx2];
+        for (j=active_nodes.succ[idx2]; j<N; j=active_nodes.succ[j]) {
+          f_single(&D_(idx2, j), D_(idx1, j) );
+          if (D_(idx2, j) < min) {
+            n_nghbr[idx2] = j;
+            min = D_(idx2, j);
+          }
+        }
+        nn_distances.update_leq(idx2, min);
+      }
+      break;
+
+    case METHOD_METR_COMPLETE:
+      /*
+        Complete linkage.
+
+        Characteristic: new distances are never shorter than the old distances.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_complete(&D_(j, idx2), D_(j, idx1) );
+        if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j])
+        f_complete(&D_(j, idx2), D_(idx1, j) );
+      // Update the distance matrix in the range (idx2, N).
+      for (j=active_nodes.succ[idx2]; j<N; j=active_nodes.succ[j])
+        f_complete(&D_(idx2, j), D_(idx1, j) );
+      break;
+
+    case METHOD_METR_AVERAGE: {
+      /*
+        Average linkage.
+
+        Shorter and longer distances can occur.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      t_float s = size1/(size1+size2);
+      t_float t = size2/(size1+size2);
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_average(&D_(j, idx2), D_(j, idx1), s, t);
+        if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_average(&D_(j, idx2), D_(idx1, j), s, t);
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        f_average(&D_(idx2, j), D_(idx1, j), s, t);
+        min = D_(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          f_average(&D_(idx2, j), D_(idx1, j), s, t);
+          if (D_(idx2,j) < min) {
+            min = D_(idx2,j);
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+    }
+
+    case METHOD_METR_WEIGHTED:
+      /*
+        Weighted linkage.
+
+        Shorter and longer distances can occur.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_weighted(&D_(j, idx2), D_(j, idx1) );
+        if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_weighted(&D_(j, idx2), D_(idx1, j) );
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        f_weighted(&D_(idx2, j), D_(idx1, j) );
+        min = D_(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          f_weighted(&D_(idx2, j), D_(idx1, j) );
+          if (D_(idx2,j) < min) {
+            min = D_(idx2,j);
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+
+    case METHOD_METR_WARD:
+      /*
+        Ward linkage.
+
+        Shorter and longer distances can occur, not smaller than min(d1,d2)
+        but maybe bigger than max(d1,d2).
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_ward(&D_(j, idx2), D_(j, idx1), mindist[idx1],
+               size1, size2, static_cast<t_float>(members[j]) );
+        if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_ward(&D_(j, idx2), D_(idx1, j), mindist[idx1], size1, size2,
+               static_cast<t_float>(members[j]) );
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        f_ward(&D_(idx2, j), D_(idx1, j), mindist[idx1],
+               size1, size2, static_cast<t_float>(members[j]) );
+        min = D_(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          f_ward(&D_(idx2, j), D_(idx1, j), mindist[idx1],
+                 size1, size2, static_cast<t_float>(members[j]) );
+          if (D_(idx2,j) < min) {
+            min = D_(idx2,j);
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+
+    case METHOD_METR_WARD_D2:
+      /*
+        Ward D2 linkage (with squared Euclidean distances).
+
+        Shorter and longer distances can occur, not smaller than min(d1,d2)
+        but maybe bigger than max(d1,d2).
+        Uses the same update formula as Ward, but with different post-processing.
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_ward(&D_(j, idx2), D_(j, idx1), mindist[idx1],
+               size1, size2, static_cast<t_float>(members[j]) );
+        if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_ward(&D_(j, idx2), D_(idx1, j), mindist[idx1], size1, size2,
+               static_cast<t_float>(members[j]) );
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        f_ward(&D_(idx2, j), D_(idx1, j), mindist[idx1],
+               size1, size2, static_cast<t_float>(members[j]) );
+        min = D_(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          f_ward(&D_(idx2, j), D_(idx1, j), mindist[idx1],
+                 size1, size2, static_cast<t_float>(members[j]) );
+          if (D_(idx2,j) < min) {
+            min = D_(idx2,j);
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+
+    case METHOD_METR_CENTROID: {
+      /*
+        Centroid linkage.
+
+        Shorter and longer distances can occur, not bigger than max(d1,d2)
+        but maybe smaller than min(d1,d2).
+      */
+      // Update the distance matrix in the range [start, idx1).
+      t_float s = size1/(size1+size2);
+      t_float t = size2/(size1+size2);
+      t_float stc = s*t*mindist[idx1];
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_centroid(&D_(j, idx2), D_(j, idx1), stc, s, t);
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+        else if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_centroid(&D_(j, idx2), D_(idx1, j), stc, s, t);
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        f_centroid(&D_(idx2, j), D_(idx1, j), stc, s, t);
+        min = D_(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          f_centroid(&D_(idx2, j), D_(idx1, j), stc, s, t);
+          if (D_(idx2,j) < min) {
+            min = D_(idx2,j);
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+    }
+
+    case METHOD_METR_MEDIAN: {
+      /*
+        Median linkage.
+
+        Shorter and longer distances can occur, not bigger than max(d1,d2)
+        but maybe smaller than min(d1,d2).
+      */
+      // Update the distance matrix in the range [start, idx1).
+      t_float c_4 = mindist[idx1]*.25;
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        f_median(&D_(j, idx2), D_(j, idx1), c_4 );
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+        else if (n_nghbr[j] == idx1)
+          n_nghbr[j] = idx2;
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for (; j<idx2; j=active_nodes.succ[j]) {
+        f_median(&D_(j, idx2), D_(idx1, j), c_4 );
+        if (D_(j, idx2) < mindist[j]) {
+          nn_distances.update_leq(j, D_(j, idx2));
+          n_nghbr[j] = idx2;
+        }
+      }
+      // Update the distance matrix in the range (idx2, N).
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        f_median(&D_(idx2, j), D_(idx1, j), c_4 );
+        min = D_(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          f_median(&D_(idx2, j), D_(idx1, j), c_4 );
+          if (D_(idx2,j) < min) {
+            min = D_(idx2,j);
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+    }
+
+    default:
+      throw std::runtime_error(std::string("Invalid method."));
+    }
+  }
+  #ifdef FE_INVALID
+  if (fetestexcept(FE_INVALID)) throw fenv_error();
+  #endif
+}
+
+/*
+  Clustering methods for vector data
+*/
+
+template <typename t_dissimilarity>
+static void MST_linkage_core_vector(const t_index N,
+                                    t_dissimilarity & dist,
+                                    cluster_result & Z2) {
+/*
+    N: integer, number of data points
+    dist: function pointer to the metric
+    Z2: output data structure
+
+    The basis of this algorithm is an algorithm by Rohlf:
+
+    F. James Rohlf, Hierarchical clustering using the minimum spanning tree,
+    The Computer Journal, vol. 16, 1973, p. 93–95.
+*/
+  t_index i;
+  t_index idx2;
+  doubly_linked_list active_nodes(N);
+  auto_array_ptr<t_float> d(N);
+
+  t_index prev_node;
+  t_float min;
+
+  // first iteration
+  idx2 = 1;
+  min = std::numeric_limits<t_float>::infinity();
+  for (i=1; i<N; ++i) {
+    d[i] = dist(0,i);
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+    if (d[i] < min) {
+      min = d[i];
+      idx2 = i;
+    }
+    else if (fc_isnan(d[i]))
+      throw (nan_error());
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+  }
+
+  Z2.append(0, idx2, min);
+
+  for (t_index j=1; j<N-1; ++j) {
+    prev_node = idx2;
+    active_nodes.remove(prev_node);
+
+    idx2 = active_nodes.succ[0];
+    min = d[idx2];
+
+    for (i=idx2; i<N; i=active_nodes.succ[i]) {
+      t_float tmp = dist(i, prev_node);
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wfloat-equal"
+#endif
+      if (d[i] > tmp)
+        d[i] = tmp;
+      else if (fc_isnan(tmp))
+        throw (nan_error());
+#if HAVE_DIAGNOSTIC
+#pragma GCC diagnostic pop
+#endif
+      if (d[i] < min) {
+        min = d[i];
+        idx2 = i;
+      }
+    }
+    Z2.append(prev_node, idx2, min);
+  }
+}
+
+template <method_codes_vector method, typename t_dissimilarity>
+static void generic_linkage_vector(const t_index N,
+                                   t_dissimilarity & dist,
+                                   cluster_result & Z2) {
+  /*
+    N: integer, number of data points
+    dist: function pointer to the metric
+    Z2: output data structure
+
+    This algorithm is valid for the distance update methods
+    "Ward", "centroid" and "median" only!
+  */
+  const t_index N_1 = N-1;
+  t_index i, j; // loop variables
+  t_index idx1, idx2; // row and column indices
+
+  auto_array_ptr<t_index> n_nghbr(N_1); // array of nearest neighbors
+  auto_array_ptr<t_float> mindist(N_1); // distances to the nearest neighbors
+  auto_array_ptr<t_index> row_repr(N); // row_repr[i]: node number that the
+                                       // i-th row represents
+  doubly_linked_list active_nodes(N);
+  binary_min_heap nn_distances(&*mindist, N_1); // minimum heap structure for
+                        // the distance to the nearest neighbor of each point
+  t_index node1, node2;     // node numbers in the output
+  t_float min; // minimum and row index for nearest-neighbor search
+
+  for (i=0; i<N; ++i)
+    // Build a list of row ↔ node label assignments.
+    // Initially i ↦ i
+    row_repr[i] = i;
+
+  // Initialize the minimal distances:
+  // Find the nearest neighbor of each point.
+  // n_nghbr[i] = argmin_{j>i} D(i,j) for i in range(N-1)
+  for (i=0; i<N_1; ++i) {
+    min = std::numeric_limits<t_float>::infinity();
+    t_index idx;
+    for (idx=j=i+1; j<N; ++j) {
+      t_float tmp;
+      switch (method) {
+      case METHOD_VECTOR_WARD:
+        tmp = dist.ward_initial(i,j);
+        break;
+      default:
+        tmp = dist.template sqeuclidean<true>(i,j);
+      }
+      if (tmp<min) {
+        min = tmp;
+        idx = j;
+      }
+    }
+    switch (method) {
+    case METHOD_VECTOR_WARD:
+      mindist[i] = t_dissimilarity::ward_initial_conversion(min);
+      break;
+    default:
+      mindist[i] = min;
+    }
+    n_nghbr[i] = idx;
+  }
+
+  // Put the minimal distances into a heap structure to make the repeated
+  // global minimum searches fast.
+  nn_distances.heapify();
+
+  // Main loop: We have N-1 merging steps.
+  for (i=0; i<N_1; ++i) {
+    idx1 = nn_distances.argmin();
+
+    while ( active_nodes.is_inactive(n_nghbr[idx1]) ) {
+      // Recompute the minimum mindist[idx1] and n_nghbr[idx1].
+      n_nghbr[idx1] = j = active_nodes.succ[idx1]; // exists, maximally N-1
+      switch (method) {
+      case METHOD_VECTOR_WARD:
+        min = dist.ward(idx1,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          t_float const tmp = dist.ward(idx1,j);
+          if (tmp<min) {
+            min = tmp;
+            n_nghbr[idx1] = j;
+          }
+        }
+        break;
+      default:
+        min = dist.template sqeuclidean<true>(idx1,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          t_float const tmp = dist.template sqeuclidean<true>(idx1,j);
+          if (tmp<min) {
+            min = tmp;
+            n_nghbr[idx1] = j;
+          }
+        }
+      }
+      /* Update the heap with the new true minimum and search for the (possibly
+         different) minimal entry. */
+      nn_distances.update_geq(idx1, min);
+      idx1 = nn_distances.argmin();
+    }
+
+    nn_distances.heap_pop(); // Remove the current minimum from the heap.
+    idx2 = n_nghbr[idx1];
+
+    // Write the newly found minimal pair of nodes to the output array.
+    node1 = row_repr[idx1];
+    node2 = row_repr[idx2];
+
+    Z2.append(node1, node2, mindist[idx1]);
+
+    switch (method) {
+    case METHOD_VECTOR_WARD:
+    case METHOD_VECTOR_CENTROID:
+      dist.merge_inplace(idx1, idx2);
+      break;
+    case METHOD_VECTOR_MEDIAN:
+      dist.merge_inplace_weighted(idx1, idx2);
+      break;
+    default:
+      throw std::runtime_error(std::string("Invalid method."));
+    }
+
+    // Index idx2 now represents the new (merged) node with label N+i.
+    row_repr[idx2] = N+i;
+    // Remove idx1 from the list of active indices (active_nodes).
+    active_nodes.remove(idx1);  // TBD later!!!
+
+    // Update the distance matrix
+    switch (method) {
+    case METHOD_VECTOR_WARD:
+      /*
+        Ward linkage.
+
+        Shorter and longer distances can occur, not smaller than min(d1,d2)
+        but maybe bigger than max(d1,d2).
+      */
+      // Update the distance matrix in the range [start, idx1).
+      for (j=active_nodes.start; j<idx1; j=active_nodes.succ[j]) {
+        if (n_nghbr[j] == idx2) {
+          n_nghbr[j] = idx1; // invalidate
+        }
+      }
+      // Update the distance matrix in the range (idx1, idx2).
+      for ( ; j<idx2; j=active_nodes.succ[j]) {
+        t_float const tmp = dist.ward(j, idx2);
+        if (tmp < mindist[j]) {
+          nn_distances.update_leq(j, tmp);
+          n_nghbr[j] = idx2;
+        }
+        else if (n_nghbr[j]==idx2) {
+          n_nghbr[j] = idx1; // invalidate
+        }
+      }
+      // Find the nearest neighbor for idx2.
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        min = dist.ward(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          t_float const tmp = dist.ward(idx2,j);
+          if (tmp < min) {
+            min = tmp;
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+      break;
+
+    default:
+      /*
+        Centroid and median linkage.
+
+        Shorter and longer distances can occur, not bigger than max(d1,d2)
+        but maybe smaller than min(d1,d2).
+      */
+      for (j=active_nodes.start; j<idx2; j=active_nodes.succ[j]) {
+        t_float const tmp = dist.template sqeuclidean<true>(j, idx2);
+        if (tmp < mindist[j]) {
+          nn_distances.update_leq(j, tmp);
+          n_nghbr[j] = idx2;
+        }
+        else if (n_nghbr[j] == idx2)
+          n_nghbr[j] = idx1; // invalidate
+      }
+      // Find the nearest neighbor for idx2.
+      if (idx2<N_1) {
+        n_nghbr[idx2] = j = active_nodes.succ[idx2]; // exists, maximally N-1
+        min = dist.template sqeuclidean<true>(idx2,j);
+        for (j=active_nodes.succ[j]; j<N; j=active_nodes.succ[j]) {
+          t_float const tmp = dist.template sqeuclidean<true>(idx2, j);
+          if (tmp < min) {
+            min = tmp;
+            n_nghbr[idx2] = j;
+          }
+        }
+        nn_distances.update(idx2, min);
+      }
+    }
+  }
+}
+
+template <method_codes_vector method, typename t_dissimilarity>
+static void generic_linkage_vector_alternative(const t_index N,
+                                               t_dissimilarity & dist,
+                                               cluster_result & Z2) {
+  /*
+    N: integer, number of data points
+    dist: function pointer to the metric
+    Z2: output data structure
+
+    This algorithm is valid for the distance update methods
+    "Ward", "centroid" and "median" only!
+  */
+  const t_index N_1 = N-1;
+  t_index i, j=0; // loop variables
+  t_index idx1, idx2; // row and column indices
+
+  auto_array_ptr<t_index> n_nghbr(2*N-2); // array of nearest neighbors
+  auto_array_ptr<t_float> mindist(2*N-2); // distances to the nearest neighbors
+
+  doubly_linked_list active_nodes(N+N_1);
+  binary_min_heap nn_distances(&*mindist, N_1, 2*N-2, 1); // minimum heap
+      // structure for the distance to the nearest neighbor of each point
+
+  t_float min; // minimum for nearest-neighbor searches
+
+  // Initialize the minimal distances:
+  // Find the nearest neighbor of each point.
+  // n_nghbr[i] = argmin_{j>i} D(i,j) for i in range(N-1)
+  for (i=1; i<N; ++i) {
+    min = std::numeric_limits<t_float>::infinity();
+    t_index idx;
+    for (idx=j=0; j<i; ++j) {
+      t_float tmp;
+      switch (method) {
+      case METHOD_VECTOR_WARD:
+        tmp = dist.ward_initial(i,j);
+        break;
+      default:
+        tmp = dist.template sqeuclidean<true>(i,j);
+      }
+      if (tmp<min) {
+        min = tmp;
+        idx = j;
+      }
+    }
+    switch (method) {
+    case METHOD_VECTOR_WARD:
+      mindist[i] = t_dissimilarity::ward_initial_conversion(min);
+      break;
+    default:
+      mindist[i] = min;
+    }
+    n_nghbr[i] = idx;
+  }
+
+  // Put the minimal distances into a heap structure to make the repeated
+  // global minimum searches fast.
+  nn_distances.heapify();
+
+  // Main loop: We have N-1 merging steps.
+  for (i=N; i<N+N_1; ++i) {
+    /*
+      The bookkeeping is different from the "stored matrix approach" algorithm
+      generic_linkage.
+
+      mindist[i] stores a lower bound on the minimum distance of the point i to
+      all points of *lower* index:
+
+          mindist[i] ≥ min_{j<i} D(i,j)
+
+      Moreover, new nodes do not re-use one of the old indices, but they are
+      given a new, unique index (SciPy convention: initial nodes are 0,…,N−1,
+      new nodes are N,…,2N−2).
+
+      Invalid nearest neighbors are not recognized by the fact that the stored
+      distance is smaller than the actual distance, but the list active_nodes
+      maintains a flag whether a node is inactive. If n_nghbr[i] points to an
+      active node, the entries nn_distances[i] and n_nghbr[i] are valid,
+      otherwise they must be recomputed.
+    */
+    idx1 = nn_distances.argmin();
+    while ( active_nodes.is_inactive(n_nghbr[idx1]) ) {
+      // Recompute the minimum mindist[idx1] and n_nghbr[idx1].
+      n_nghbr[idx1] = j = active_nodes.start;
+      switch (method) {
+      case METHOD_VECTOR_WARD:
+        min = dist.ward_extended(idx1,j);
+        for (j=active_nodes.succ[j]; j<idx1; j=active_nodes.succ[j]) {
+          t_float tmp = dist.ward_extended(idx1,j);
+          if (tmp<min) {
+            min = tmp;
+            n_nghbr[idx1] = j;
+          }
+        }
+        break;
+      default:
+        min = dist.sqeuclidean_extended(idx1,j);
+        for (j=active_nodes.succ[j]; j<idx1; j=active_nodes.succ[j]) {
+          t_float const tmp = dist.sqeuclidean_extended(idx1,j);
+          if (tmp<min) {
+            min = tmp;
+            n_nghbr[idx1] = j;
+          }
+        }
+      }
+      /* Update the heap with the new true minimum and search for the (possibly
+         different) minimal entry. */
+      nn_distances.update_geq(idx1, min);
+      idx1 = nn_distances.argmin();
+    }
+
+    idx2 = n_nghbr[idx1];
+    active_nodes.remove(idx1);
+    active_nodes.remove(idx2);
+
+    Z2.append(idx1, idx2, mindist[idx1]);
+
+    if (i<2*N_1) {
+      switch (method) {
+      case METHOD_VECTOR_WARD:
+      case METHOD_VECTOR_CENTROID:
+        dist.merge(idx1, idx2, i);
+        break;
+
+      case METHOD_VECTOR_MEDIAN:
+        dist.merge_weighted(idx1, idx2, i);
+        break;
+
+      default:
+        throw std::runtime_error(std::string("Invalid method."));
+      }
+
+      n_nghbr[i] = active_nodes.start;
+      if (method==METHOD_VECTOR_WARD) {
+        /*
+          Ward linkage.
+
+          Shorter and longer distances can occur, not smaller than min(d1,d2)
+          but maybe bigger than max(d1,d2).
+        */
+        min = dist.ward_extended(active_nodes.start, i);
+        for (j=active_nodes.succ[active_nodes.start]; j<i;
+             j=active_nodes.succ[j]) {
+          t_float tmp = dist.ward_extended(j, i);
+          if (tmp < min) {
+            min = tmp;
+            n_nghbr[i] = j;
+          }
+        }
+      }
+      else {
+        /*
+          Centroid and median linkage.
+
+          Shorter and longer distances can occur, not bigger than max(d1,d2)
+          but maybe smaller than min(d1,d2).
+        */
+        min = dist.sqeuclidean_extended(active_nodes.start, i);
+        for (j=active_nodes.succ[active_nodes.start]; j<i;
+             j=active_nodes.succ[j]) {
+          t_float tmp = dist.sqeuclidean_extended(j, i);
+          if (tmp < min) {
+            min = tmp;
+            n_nghbr[i] = j;
+          }
+        }
+      }
+      if (idx2<active_nodes.start)  {
+        nn_distances.remove(active_nodes.start);
+      } else {
+        nn_distances.remove(idx2);
+      }
+      nn_distances.replace(idx1, i, min);
+    }
+  }
+}
+
+#if HAVE_VISIBILITY
+#pragma GCC visibility pop
+#endif