leafordering.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "using Clustering\n",
    "using Distances\n",
    "using BenchmarkTools;"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5000×5000 Array{Float64,2}:\n",
       " 0.0       0.343369  0.34366   0.340141  …  0.336091  0.338619  0.333748\n",
       " 0.343369  0.0       0.331632  0.335547     0.335049  0.338414  0.339493\n",
       " 0.34366   0.331632  0.0       0.335141     0.339824  0.34027   0.338529\n",
       " 0.340141  0.335547  0.335141  0.0          0.322269  0.327231  0.340499\n",
       " 0.338945  0.335581  0.342374  0.332958     0.330955  0.325538  0.328526\n",
       " 0.343973  0.340117  0.344257  0.33879   …  0.337204  0.316357  0.32182 \n",
       " 0.327998  0.333916  0.335018  0.334355     0.340203  0.335612  0.334887\n",
       " 0.326519  0.337853  0.346471  0.344228     0.327721  0.334557  0.319285\n",
       " 0.330871  0.329097  0.348236  0.33656      0.332745  0.334408  0.33932 \n",
       " 0.339208  0.347929  0.335793  0.346454     0.330397  0.340416  0.336861\n",
       " 0.341503  0.345218  0.331044  0.323576  …  0.325335  0.33884   0.332917\n",
       " 0.322232  0.330622  0.330086  0.328989     0.334396  0.336174  0.317607\n",
       " 0.339902  0.342281  0.342619  0.347962     0.333823  0.351439  0.338163\n",
       " ⋮                                       ⋱                              \n",
       " 0.330957  0.347526  0.331785  0.335055     0.342946  0.338383  0.341168\n",
       " 0.327584  0.334309  0.324169  0.321827     0.331287  0.335389  0.318614\n",
       " 0.327557  0.32448   0.328454  0.329129  …  0.339167  0.344099  0.338294\n",
       " 0.335319  0.34019   0.330957  0.340505     0.330014  0.338275  0.323959\n",
       " 0.32913   0.32356   0.332591  0.336012     0.335383  0.334236  0.321879\n",
       " 0.340549  0.33668   0.350206  0.333848     0.32995   0.345196  0.325663\n",
       " 0.32749   0.329868  0.332984  0.337432     0.33624   0.334221  0.328347\n",
       " 0.33659   0.329371  0.333425  0.338162  …  0.338806  0.328651  0.341408\n",
       " 0.335656  0.332368  0.341622  0.342993     0.332729  0.346547  0.337752\n",
       " 0.336091  0.335049  0.339824  0.322269     0.0       0.336087  0.323557\n",
       " 0.338619  0.338414  0.34027   0.327231     0.336087  0.0       0.32873 \n",
       " 0.333748  0.339493  0.338529  0.340499     0.323557  0.32873   0.0     "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = rand(1000, 5000)\n",
    "dm = pairwise(BrayCurtis(), m)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "BenchmarkTools.Trial: \n",
       "  memory estimate:  289.31 MiB\n",
       "  allocs estimate:  201803\n",
       "  --------------\n",
       "  minimum time:     1.016 s (10.77% GC)\n",
       "  median time:      1.038 s (10.54% GC)\n",
       "  mean time:        1.067 s (10.66% GC)\n",
       "  maximum time:     1.139 s (12.37% GC)\n",
       "  --------------\n",
       "  samples:          5\n",
       "  evals/sample:     1"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "@benchmark hcl = hclust(dm, :single)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5000-element Array{Int64,1}:\n",
       " 2700\n",
       "  682\n",
       " 4876\n",
       " 4870\n",
       " 2919\n",
       "  253\n",
       " 1916\n",
       " 2757\n",
       " 4303\n",
       " 3086\n",
       " 1046\n",
       " 3008\n",
       " 2071\n",
       "    ⋮\n",
       " 4858\n",
       " 2674\n",
       " 3959\n",
       " 4513\n",
       " 3780\n",
       " 3829\n",
       " 3388\n",
       " 1216\n",
       " 3249\n",
       " 4103\n",
       " 3213\n",
       " 4250"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hcl = hclust(dm, :single)\n",
    "hcl.order"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "BenchmarkTools.Trial: \n",
       "  memory estimate:  25.01 MiB\n",
       "  allocs estimate:  51788\n",
       "  --------------\n",
       "  minimum time:     43.757 ms (3.91% GC)\n",
       "  median time:      48.536 ms (4.61% GC)\n",
       "  mean time:        49.039 ms (4.86% GC)\n",
       "  maximum time:     59.522 ms (5.77% GC)\n",
       "  --------------\n",
       "  samples:          102\n",
       "  evals/sample:     1"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "@benchmark optimalorder(hcl, dm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5000-element Array{Int64,1}:\n",
       " 2700\n",
       "  543\n",
       " 4250\n",
       " 4653\n",
       " 4195\n",
       " 4825\n",
       " 4561\n",
       " 2784\n",
       " 2874\n",
       "  634\n",
       "  398\n",
       " 3020\n",
       " 2250\n",
       "    ⋮\n",
       "  860\n",
       " 1967\n",
       " 2408\n",
       " 4268\n",
       " 3121\n",
       " 1469\n",
       " 2071\n",
       " 3008\n",
       " 3086\n",
       "  253\n",
       " 4870\n",
       " 4876"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "optimalorder(hcl, dm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Julia 0.6.1",
   "language": "julia",
   "name": "julia-0.6"
  },
  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
   "version": "0.6.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}