One last check on unknowns, these will now be weeded out in statistics.csv generation.

notebooks/ToL_EDA.ipynb

@@ -22,7 +22,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_65691/3694103411.py:1: DtypeWarning: Columns (4,5,6) have mixed types. Specify dtype option on import or set low_memory=False.\n",
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_88978/3694103411.py:1: DtypeWarning: Columns (4,5,6) have mixed types. Specify dtype option on import or set low_memory=False.\n",
       "  df = pd.read_csv(\"../data/v1-dev-names.csv\")\n"
      ]
     }
@@ -345,6 +345,325 @@
     "`Metazoa` and `Animalia` overlap, as do `Archaeplastida` and `Plantae`. They are sometimes used interchangably, though the former of each is a newer (more refined?) designation. Later we'll see this distinction cuts is by our data sources."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "One more oddity to note: we have about 84K images with genus labeled \"UNKNOWN\"."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 84025 entries, 30 to 10436423\n",
+      "Data columns (total 16 columns):\n",
+      " #   Column            Non-Null Count  Dtype  \n",
+      "---  ------            --------------  -----  \n",
+      " 0   treeoflife_id     84025 non-null  object \n",
+      " 1   eol_content_id    84025 non-null  float64\n",
+      " 2   eol_page_id       84025 non-null  float64\n",
+      " 3   bioscan_part      0 non-null      float64\n",
+      " 4   bioscan_filename  0 non-null      object \n",
+      " 5   inat21_filename   0 non-null      object \n",
+      " 6   inat21_cls_name   0 non-null      object \n",
+      " 7   inat21_cls_num    0 non-null      float64\n",
+      " 8   kingdom           0 non-null      object \n",
+      " 9   phylum            0 non-null      object \n",
+      " 10  class             0 non-null      object \n",
+      " 11  order             0 non-null      object \n",
+      " 12  family            0 non-null      object \n",
+      " 13  genus             84025 non-null  object \n",
+      " 14  species           7 non-null      object \n",
+      " 15  common            84025 non-null  object \n",
+      "dtypes: float64(4), object(12)\n",
+      "memory usage: 10.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "df.loc[df.genus.str.lower() == \"unknown\"].info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Check in on the few non-null species values."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
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+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>treeoflife_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>bioscan_part</th>\n",
+       "      <th>bioscan_filename</th>\n",
+       "      <th>inat21_filename</th>\n",
+       "      <th>inat21_cls_name</th>\n",
+       "      <th>inat21_cls_num</th>\n",
+       "      <th>kingdom</th>\n",
+       "      <th>phylum</th>\n",
+       "      <th>class</th>\n",
+       "      <th>order</th>\n",
+       "      <th>family</th>\n",
+       "      <th>genus</th>\n",
+       "      <th>species</th>\n",
+       "      <th>common</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>302277</th>\n",
+       "      <td>1295e061-064b-4616-a10f-4a546489eb1a</td>\n",
+       "      <td>14046024.0</td>\n",
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+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Unknown</td>\n",
+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
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+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Unknown</td>\n",
+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1133612</th>\n",
+       "      <td>08614858-7836-4543-a33c-0432b85d8455</td>\n",
+       "      <td>14046025.0</td>\n",
+       "      <td>62660090.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Unknown</td>\n",
+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1490749</th>\n",
+       "      <td>73076cbf-3e79-427b-b0cb-5ba45386bb60</td>\n",
+       "      <td>14046026.0</td>\n",
+       "      <td>62660090.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Unknown</td>\n",
+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3686711</th>\n",
+       "      <td>79212ef1-bf62-4e1f-b983-4fb6d4bd6523</td>\n",
+       "      <td>14046028.0</td>\n",
+       "      <td>62660090.0</td>\n",
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+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
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+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Unknown</td>\n",
+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4036030</th>\n",
+       "      <td>1aeaf888-130b-4606-b9c6-f16bbcbbb68f</td>\n",
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+       "      <td>62660090.0</td>\n",
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+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
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+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4526299</th>\n",
+       "      <td>be856027-d6c7-4321-b0d3-a155ad5b49ba</td>\n",
+       "      <td>14046029.0</td>\n",
+       "      <td>62660090.0</td>\n",
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+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Unknown</td>\n",
+       "      <td>pleasehelp</td>\n",
+       "      <td>Unknown pleasehelp</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                                treeoflife_id  eol_content_id  eol_page_id   \n",
+       "302277   1295e061-064b-4616-a10f-4a546489eb1a      14046024.0   62660090.0  \\\n",
+       "662535   79159008-2108-4690-a9b2-9812e0247ea5      14046023.0   62660090.0   \n",
+       "1133612  08614858-7836-4543-a33c-0432b85d8455      14046025.0   62660090.0   \n",
+       "1490749  73076cbf-3e79-427b-b0cb-5ba45386bb60      14046026.0   62660090.0   \n",
+       "3686711  79212ef1-bf62-4e1f-b983-4fb6d4bd6523      14046028.0   62660090.0   \n",
+       "4036030  1aeaf888-130b-4606-b9c6-f16bbcbbb68f      14046027.0   62660090.0   \n",
+       "4526299  be856027-d6c7-4321-b0d3-a155ad5b49ba      14046029.0   62660090.0   \n",
+       "\n",
+       "         bioscan_part bioscan_filename inat21_filename inat21_cls_name   \n",
+       "302277            NaN              NaN             NaN             NaN  \\\n",
+       "662535            NaN              NaN             NaN             NaN   \n",
+       "1133612           NaN              NaN             NaN             NaN   \n",
+       "1490749           NaN              NaN             NaN             NaN   \n",
+       "3686711           NaN              NaN             NaN             NaN   \n",
+       "4036030           NaN              NaN             NaN             NaN   \n",
+       "4526299           NaN              NaN             NaN             NaN   \n",
+       "\n",
+       "         inat21_cls_num kingdom phylum class order family    genus   \n",
+       "302277              NaN     NaN    NaN   NaN   NaN    NaN  Unknown  \\\n",
+       "662535              NaN     NaN    NaN   NaN   NaN    NaN  Unknown   \n",
+       "1133612             NaN     NaN    NaN   NaN   NaN    NaN  Unknown   \n",
+       "1490749             NaN     NaN    NaN   NaN   NaN    NaN  Unknown   \n",
+       "3686711             NaN     NaN    NaN   NaN   NaN    NaN  Unknown   \n",
+       "4036030             NaN     NaN    NaN   NaN   NaN    NaN  Unknown   \n",
+       "4526299             NaN     NaN    NaN   NaN   NaN    NaN  Unknown   \n",
+       "\n",
+       "            species              common  \n",
+       "302277   pleasehelp  Unknown pleasehelp  \n",
+       "662535   pleasehelp  Unknown pleasehelp  \n",
+       "1133612  pleasehelp  Unknown pleasehelp  \n",
+       "1490749  pleasehelp  Unknown pleasehelp  \n",
+       "3686711  pleasehelp  Unknown pleasehelp  \n",
+       "4036030  pleasehelp  Unknown pleasehelp  \n",
+       "4526299  pleasehelp  Unknown pleasehelp  "
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_unknown_genus = df.loc[df.genus.str.lower() == \"unknown\"]\n",
+    "df_unknown_genus.loc[df_unknown_genus.species.notna()]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Would be interesting to see what the model thinks of these once we re-train. They're all some kind of blue dragonfly-like bug ([eol page](https://eol.org/pages/62660090/media))."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "7"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(df.loc[df.species.str.lower() == \"pleasehelp\"])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Good only these 7."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -3792,7 +4111,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "venv",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -3807,8 +4126,7 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.11.3"
-  },
-  "orig_nbformat": 4
+  }
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