Species clean order by similarity.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
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   },
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from fuzzyutil import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('names_v4.csv', encoding='latin1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
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       "    .dataframe thead th {\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>Taxonomy</th>\n",
       "      <th>freq</th>\n",
       "      <th>last_seen</th>\n",
       "      <th>To_name</th>\n",
       "      <th>Status</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>Epizooanthidae</td>\n",
       "      <td>1</td>\n",
       "      <td>107</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>Lebensspuren (echinoderm bulldozing tracks)</td>\n",
       "      <td>1</td>\n",
       "      <td>112</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>Paguridae</td>\n",
       "      <td>1</td>\n",
       "      <td>112</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>Porifera, apricot incrusting</td>\n",
       "      <td>1</td>\n",
       "      <td>161</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>Porifera, many osculi</td>\n",
       "      <td>1</td>\n",
       "      <td>161</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      "text/plain": [
       "   Unnamed: 0                                      Taxonomy  freq  last_seen  \\\n",
       "0           1                                Epizooanthidae     1        107   \n",
       "1           2   Lebensspuren (echinoderm bulldozing tracks)     1        112   \n",
       "2           3                                     Paguridae     1        112   \n",
       "3           4                  Porifera, apricot incrusting     1        161   \n",
       "4           5                         Porifera, many osculi     1        161   \n",
       "\n",
       "  To_name  Status  \n",
       "0     NaN   False  \n",
       "1     NaN   False  \n",
       "2     NaN   False  \n",
       "3     NaN   False  \n",
       "4     NaN   False  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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      "text/plain": [
       "8289"
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     },
     "execution_count": 5,
     "metadata": {},
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   ],
   "source": [
    "len(df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "allspecies = df['Taxonomy'][df['Status']==False]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "8073"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(allspecies)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Reorder list of elements according to their relative distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "results = similorder(allspecies, scorelimit=99, method='token_set', verbose=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "100"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(results)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "toadj = getcorrections(results)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
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   "source": [
    "toadj"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7448"
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     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "len(results)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "corrected = toadj.get_changed_df()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "corrected"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<function fuzzyutil.getcorrections(toadjust, to_correct='to_correct', corrected='corrected')>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "getcorrections"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'list' object has no attribute 'to_csv'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-18-c18cead26d21>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mresults\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'names_v4_false_ordered.csv'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindex\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m: 'list' object has no attribute 'to_csv'"
     ]
    }
   ],
   "source": [
    "results.to_csv('names_v4_false_ordered.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "myresults = pd.DataFrame(results)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "myresults.to_csv('myresults.csv', index=False, header=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " Epizooanthidae\n",
      "epizooanthidae on Paguridae\n",
      "Paguridae with epizooanthidae\n",
      "Paguridae like\n",
      " Paguridae\n",
      "Paguridae\n",
      "Pandalidae\n",
      "Pandalidae red\n",
      "pandalidae red\n",
      "Crangonidae/Pandalidae\n"
     ]
    }
   ],
   "source": [
    "!head myresults.csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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