Wolbachia Analysis.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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     "output_type": "stream",
     "text": [
      "WARNING (theano.sandbox.cuda): CUDA is installed, but device gpu0 is not available  (error: Unable to get the number of gpus available: CUDA driver version is insufficient for CUDA runtime version)\n"
     ]
    }
   ],
   "source": [
    "from fetch import *\n",
    "from network_analysis import create_corpus, LDA_topics, get_top_topics_by_year"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
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   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Fetching results for Wolbachia mosquito\n",
      "Found 424 items\n"
     ]
    }
   ],
   "source": [
    "S = SearchAndCapture('fccoelho@gmail.com', 'Wolbachia mosquito', collection=\"wolbachia\")\n",
    "S.update_multiple_searches(['Wolbachia mosquito'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "corpus, dic = create_corpus('wolbachia')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "lda = LDA_topics(corpus, dic, 15)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/lib/python3.5/dist-packages/funcy/decorators.py:56: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead\n",
      "  spec = inspect.getargspec(func)\n",
      "/usr/local/lib/python3.5/dist-packages/funcy/decorators.py:56: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead\n",
      "  spec = inspect.getargspec(func)\n",
      "/usr/local/lib/python3.5/dist-packages/funcy/decorators.py:56: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead\n",
      "  spec = inspect.getargspec(func)\n",
      "/usr/local/lib/python3.5/dist-packages/funcy/decorators.py:56: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead\n",
      "  spec = inspect.getargspec(func)\n",
      "/usr/local/lib/python3.5/dist-packages/funcy/decorators.py:56: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead\n",
      "  spec = inspect.getargspec(func)\n",
      "/usr/local/lib/python3.5/dist-packages/funcy/decorators.py:56: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead\n",
      "  spec = inspect.getargspec(func)\n"
     ]
    }
   ],
   "source": [
    "import pyLDAvis.gensim as gensimvis\n",
    "import pyLDAvis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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[-0.0063800404981302575, 0.007252973057786221, -0.08349164343017373, -0.02004255454046528, 0.04237676788832711, -0.07752067008563691, 0.051694310636994194, -0.029349857392310042, 0.16582902962767063, -0.13482443385984824, 0.021675667001093916, 0.03210875750900393, 0.11723183942517072, 0.05715372515905611, -0.1437138704985379], \"x\": [-0.052781196971298724, 0.0992266251184675, 0.0649843217997038, 0.09349315239920401, -0.13336708355261995, 0.06317888696196475, -0.07382909182895651, -0.020606831393742253, 0.2027452127137657, 0.004947610692064068, -0.09459520747670969, 0.050645915414431864, -0.05942473565021474, -0.131144596878252, -0.013472981347807483], \"cluster\": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]}};\n",
       "\n",
       "function LDAvis_load_lib(url, callback){\n",
       "  var s = document.createElement('script');\n",
       "  s.src = url;\n",
       "  s.async = true;\n",
       "  s.onreadystatechange = s.onload = callback;\n",
       "  s.onerror = function(){console.warn(\"failed to load library \" + url);};\n",
       "  document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "}\n",
       "\n",
       "if(typeof(LDAvis) !== \"undefined\"){\n",
       "   // already loaded: just create the visualization\n",
       "   !function(LDAvis){\n",
       "       new LDAvis(\"#\" + \"ldavis_el293761403418338656408256431004\", ldavis_el293761403418338656408256431004_data);\n",
       "   }(LDAvis);\n",
       "}else if(typeof define === \"function\" && define.amd){\n",
       "   // require.js is available: use it to load d3/LDAvis\n",
       "   require.config({paths: {d3: \"https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min\"}});\n",
       "   require([\"d3\"], function(d3){\n",
       "      window.d3 = d3;\n",
       "      LDAvis_load_lib(\"https://cdn.rawgit.com/bmabey/pyLDAvis/files/ldavis.v1.0.0.js\", function(){\n",
       "        new LDAvis(\"#\" + \"ldavis_el293761403418338656408256431004\", ldavis_el293761403418338656408256431004_data);\n",
       "      });\n",
       "    });\n",
       "}else{\n",
       "    // require.js not available: dynamically load d3 & LDAvis\n",
       "    LDAvis_load_lib(\"https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js\", function(){\n",
       "         LDAvis_load_lib(\"https://cdn.rawgit.com/bmabey/pyLDAvis/files/ldavis.v1.0.0.js\", function(){\n",
       "                 new LDAvis(\"#\" + \"ldavis_el293761403418338656408256431004\", ldavis_el293761403418338656408256431004_data);\n",
       "            })\n",
       "         });\n",
       "}\n",
       "</script>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vis_data = gensimvis.prepare(lda, corpus, dic)\n",
    "pyLDAvis.display(vis_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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       " [(1, 0.62454202106989087),\n",
       "  (4, 0.28153833788236693),\n",
       "  (14, 0.075916938102444514),\n",
       "  (3, 0.012649892812931381)],\n",
       " [(9, 0.59171221734642421),\n",
       "  (13, 0.23405458953297509),\n",
       "  (8, 0.12897460706795202),\n",
       "  (1, 0.039344597385542947)],\n",
       " [(4, 0.75919026358408892), (1, 0.23314010810728594)],\n",
       " [(11, 0.97964303660755681), (10, 0.016775689415341768)],\n",
       " [(1, 0.87061947021370489), (11, 0.11906305238636003)],\n",
       " [(1, 0.87623261722760237), (6, 0.11753235939374675)],\n",
       " [(1, 0.60951110131446207),\n",
       "  (9, 0.25843208265140527),\n",
       "  (11, 0.12575758883174395)],\n",
       " [(11, 0.6772890513224431), (14, 0.30826647424187992)],\n",
       " [(8, 0.87965884587649401), (11, 0.112933739157625)],\n",
       " [(11, 0.57942143449228267), (10, 0.40695954598627321)],\n",
       " [(0, 0.42967197534238877),\n",
       "  (12, 0.27938252247398315),\n",
       "  (14, 0.23185001427234037),\n",
       "  (10, 0.043635611265175428),\n",
       "  (9, 0.010331661997961967)],\n",
       " [(1, 0.99265090639105014)],\n",
       " [(1, 0.62297750846917721),\n",
       "  (9, 0.28955406764401592),\n",
       "  (0, 0.078866256535277277)],\n",
       " [(1, 0.72443289958122681),\n",
       "  (10, 0.15527394420922072),\n",
       "  (11, 0.11260083011714585)],\n",
       " [(3, 0.99037798476565675)],\n",
       " [(9, 0.99276484663221409)],\n",
       " [(14, 0.50581739675239434),\n",
       "  (9, 0.27565880761610556),\n",
       "  (5, 0.20827905441367275)],\n",
       " [(6, 0.32569936950991291),\n",
       "  (0, 0.25891508284336151),\n",
       "  (14, 0.22481116522617947),\n",
       "  (2, 0.18475426566348177)],\n",
       " [(0, 0.47129555346664692),\n",
       "  (2, 0.22225270951163162),\n",
       "  (4, 0.15265835401326422),\n",
       "  (14, 0.14736062171780032)],\n",
       " [(14, 0.60392740559195779), (6, 0.38940591481572323)],\n",
       " [(3, 0.43127159059707887),\n",
       "  (0, 0.42416649597794975),\n",
       "  (10, 0.13468535785555111)]]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "doc_topics = get_top_topics_by_year(lda, dic,'wolbachia',2016)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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