diff --git "a/notebooks/BioCLIP_data_viz.ipynb" "b/notebooks/BioCLIP_data_viz.ipynb"
new file mode 100644--- /dev/null
+++ "b/notebooks/BioCLIP_data_viz.ipynb"
@@ -0,0 +1,3250 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import seaborn as sns\n",
+ "import plotly.express as px\n",
+ "\n",
+ "sns.set_style(\"whitegrid\")\n",
+ "sns.set(rc = {'figure.figsize': (10,10)})"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_222484/3694103411.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"
+ ]
+ }
+ ],
+ "source": [
+ "df = pd.read_csv(\"../data/v1-dev-names.csv\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "
\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " treeoflife_id | \n",
+ " eol_content_id | \n",
+ " eol_page_id | \n",
+ " bioscan_part | \n",
+ " bioscan_filename | \n",
+ " inat21_filename | \n",
+ " inat21_cls_name | \n",
+ " inat21_cls_num | \n",
+ " kingdom | \n",
+ " phylum | \n",
+ " class | \n",
+ " order | \n",
+ " family | \n",
+ " genus | \n",
+ " species | \n",
+ " common | \n",
+ "
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+ " \n",
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+ " NaN | \n",
+ " NaN | \n",
+ " Manfreda | \n",
+ " NaN | \n",
+ " tuberose | \n",
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+ " \n",
+ " | 1 | \n",
+ " 5ca08f6b-9396-4cb9-9283-8dee158aac18 | \n",
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+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " Metazoa | \n",
+ " Arthropoda | \n",
+ " Pancrustacea | \n",
+ " Lepidoptera | \n",
+ " Oenosandridae | \n",
+ " Discophlebia | \n",
+ " lipauges | \n",
+ " Discophlebia lipauges | \n",
+ "
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+ " \n",
+ " | 2 | \n",
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+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " Archaeplastida | \n",
+ " Tracheophyta | \n",
+ " NaN | \n",
+ " Sapindales | \n",
+ " Rutaceae | \n",
+ " Melicope | \n",
+ " denhamii | \n",
+ " Melicope denhamii | \n",
+ "
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+ " \n",
+ " | 3 | \n",
+ " 1f53e9d1-527f-42fd-b813-9f62fa2c2372 | \n",
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+ " 607817.0 | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " Metazoa | \n",
+ " Arthropoda | \n",
+ " Pancrustacea | \n",
+ " Trichoptera | \n",
+ " Limnephilidae | \n",
+ " Limnephilus | \n",
+ " lithus | \n",
+ " Limnephilus lithus | \n",
+ "
\n",
+ " \n",
+ " | 4 | \n",
+ " a05bc2a8-5453-4683-903e-ed44f0fe7245 | \n",
+ " 20300703.0 | \n",
+ " 267922.0 | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " Anatolian Black-eyed Blue | \n",
+ "
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+ " \n",
+ "
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+ "
"
+ ],
+ "text/plain": [
+ " treeoflife_id eol_content_id eol_page_id \\\n",
+ "0 0824741f-cc1c-4881-b292-15fd3f7964cd 29538374.0 65414274.0 \n",
+ "1 5ca08f6b-9396-4cb9-9283-8dee158aac18 27793900.0 888015.0 \n",
+ "2 f8c0f271-d8e5-4299-92d3-920508f74bf0 29121641.0 5618956.0 \n",
+ "3 1f53e9d1-527f-42fd-b813-9f62fa2c2372 27596176.0 607817.0 \n",
+ "4 a05bc2a8-5453-4683-903e-ed44f0fe7245 20300703.0 267922.0 \n",
+ "\n",
+ " bioscan_part bioscan_filename inat21_filename inat21_cls_name \\\n",
+ "0 NaN NaN NaN NaN \n",
+ "1 NaN NaN NaN NaN \n",
+ "2 NaN NaN NaN NaN \n",
+ "3 NaN NaN NaN NaN \n",
+ "4 NaN NaN NaN NaN \n",
+ "\n",
+ " inat21_cls_num kingdom phylum class order \\\n",
+ "0 NaN NaN NaN NaN NaN \n",
+ "1 NaN Metazoa Arthropoda Pancrustacea Lepidoptera \n",
+ "2 NaN Archaeplastida Tracheophyta NaN Sapindales \n",
+ "3 NaN Metazoa Arthropoda Pancrustacea Trichoptera \n",
+ "4 NaN NaN NaN NaN NaN \n",
+ "\n",
+ " family genus species common \n",
+ "0 NaN Manfreda NaN tuberose \n",
+ "1 Oenosandridae Discophlebia lipauges Discophlebia lipauges \n",
+ "2 Rutaceae Melicope denhamii Melicope denhamii \n",
+ "3 Limnephilidae Limnephilus lithus Limnephilus lithus \n",
+ "4 NaN NaN NaN Anatolian Black-eyed Blue "
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df.head()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "RangeIndex: 10436521 entries, 0 to 10436520\n",
+ "Data columns (total 16 columns):\n",
+ " # Column Non-Null Count Dtype \n",
+ "--- ------ -------------- ----- \n",
+ " 0 treeoflife_id 10436521 non-null object \n",
+ " 1 eol_content_id 6621365 non-null float64\n",
+ " 2 eol_page_id 6621365 non-null float64\n",
+ " 3 bioscan_part 1128313 non-null float64\n",
+ " 4 bioscan_filename 1128313 non-null object \n",
+ " 5 inat21_filename 2686843 non-null object \n",
+ " 6 inat21_cls_name 2686843 non-null object \n",
+ " 7 inat21_cls_num 2686843 non-null float64\n",
+ " 8 kingdom 7734559 non-null object \n",
+ " 9 phylum 7732689 non-null object \n",
+ " 10 class 6657484 non-null object \n",
+ " 11 order 7690349 non-null object \n",
+ " 12 family 7706759 non-null object \n",
+ " 13 genus 8060829 non-null object \n",
+ " 14 species 7179863 non-null object \n",
+ " 15 common 10436521 non-null object \n",
+ "dtypes: float64(4), object(12)\n",
+ "memory usage: 1.2+ GB\n"
+ ]
+ }
+ ],
+ "source": [
+ "df.info(show_counts = True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Do we truly have common name labeled for all images?\n",
+ "\n",
+ "Sometimes it is the scientific name."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "treeoflife_id 10436521\n",
+ "eol_content_id 6621365\n",
+ "eol_page_id 570515\n",
+ "bioscan_part 113\n",
+ "bioscan_filename 1128313\n",
+ "inat21_filename 2686843\n",
+ "inat21_cls_name 10000\n",
+ "inat21_cls_num 10000\n",
+ "kingdom 5\n",
+ "phylum 49\n",
+ "class 136\n",
+ "order 766\n",
+ "family 5665\n",
+ "genus 89914\n",
+ "species 189846\n",
+ "common 527316\n",
+ "dtype: int64"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df.nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa = list(df.columns[8:15])\n",
+ "taxa"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Check the number of images with all 7 taxonomic labels."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Index: 6657484 entries, 1 to 10436518\n",
+ "Data columns (total 7 columns):\n",
+ " # Column Non-Null Count Dtype \n",
+ "--- ------ -------------- ----- \n",
+ " 0 kingdom 6657484 non-null object\n",
+ " 1 phylum 6657484 non-null object\n",
+ " 2 class 6657484 non-null object\n",
+ " 3 order 6615972 non-null object\n",
+ " 4 family 6630424 non-null object\n",
+ " 5 genus 5691848 non-null object\n",
+ " 6 species 5267629 non-null object\n",
+ "dtypes: object(7)\n",
+ "memory usage: 406.3+ MB\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Class has least non-null entries, so we'll start by filtering it out\n",
+ "df_all_taxa = df.loc[df['class'].notna()]\n",
+ "df_all_taxa[taxa].info(show_counts = True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Index: 5267629 entries, 1 to 10436518\n",
+ "Data columns (total 7 columns):\n",
+ " # Column Non-Null Count Dtype \n",
+ "--- ------ -------------- ----- \n",
+ " 0 kingdom 5267629 non-null object\n",
+ " 1 phylum 5267629 non-null object\n",
+ " 2 class 5267629 non-null object\n",
+ " 3 order 5233623 non-null object\n",
+ " 4 family 5261785 non-null object\n",
+ " 5 genus 5267456 non-null object\n",
+ " 6 species 5267629 non-null object\n",
+ "dtypes: object(7)\n",
+ "memory usage: 321.5+ MB\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Now species has least non-null values\n",
+ "df_all_taxa = df_all_taxa.loc[df_all_taxa['species'].notna()]\n",
+ "df_all_taxa[taxa].info(show_counts = True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Index: 5233623 entries, 1 to 10436518\n",
+ "Data columns (total 7 columns):\n",
+ " # Column Non-Null Count Dtype \n",
+ "--- ------ -------------- ----- \n",
+ " 0 kingdom 5233623 non-null object\n",
+ " 1 phylum 5233623 non-null object\n",
+ " 2 class 5233623 non-null object\n",
+ " 3 order 5233623 non-null object\n",
+ " 4 family 5228644 non-null object\n",
+ " 5 genus 5233450 non-null object\n",
+ " 6 species 5233623 non-null object\n",
+ "dtypes: object(7)\n",
+ "memory usage: 319.4+ MB\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Now order has least non-null values \n",
+ "df_all_taxa = df_all_taxa.loc[df_all_taxa['order'].notna()]\n",
+ "df_all_taxa[taxa].info(show_counts = True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Index: 5228644 entries, 1 to 10436518\n",
+ "Data columns (total 7 columns):\n",
+ " # Column Non-Null Count Dtype \n",
+ "--- ------ -------------- ----- \n",
+ " 0 kingdom 5228644 non-null object\n",
+ " 1 phylum 5228644 non-null object\n",
+ " 2 class 5228644 non-null object\n",
+ " 3 order 5228644 non-null object\n",
+ " 4 family 5228644 non-null object\n",
+ " 5 genus 5228471 non-null object\n",
+ " 6 species 5228644 non-null object\n",
+ "dtypes: object(7)\n",
+ "memory usage: 319.1+ MB\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Now family has least non-null values\n",
+ "df_all_taxa = df_all_taxa.loc[df_all_taxa['family'].notna()]\n",
+ "df_all_taxa[taxa].info(show_counts = True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Index: 5228471 entries, 1 to 10436518\n",
+ "Data columns (total 7 columns):\n",
+ " # Column Non-Null Count Dtype \n",
+ "--- ------ -------------- ----- \n",
+ " 0 kingdom 5228471 non-null object\n",
+ " 1 phylum 5228471 non-null object\n",
+ " 2 class 5228471 non-null object\n",
+ " 3 order 5228471 non-null object\n",
+ " 4 family 5228471 non-null object\n",
+ " 5 genus 5228471 non-null object\n",
+ " 6 species 5228471 non-null object\n",
+ "dtypes: object(7)\n",
+ "memory usage: 319.1+ MB\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Finally, genus is the only one with null values\n",
+ "df_all_taxa = df_all_taxa.loc[df_all_taxa['genus'].notna()]\n",
+ "df_all_taxa[taxa].info(show_counts = True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We have 5,228,471 images with full taxonomic labels."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### Distributions\n",
+ "\n",
+ "Work through larger number of unique taxa here, on server. Also, make `df_taxa` with just taxa columns so it's smaller to process faster.\n",
+ "\n",
+ "All in format `num_lowerTaxon_higherTaxon`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "df_taxa = df[taxa]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Species per higher order taxa will take longest."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Let's start with the taxa that have more unique values under kingdom to see where the server's at on speed too."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_families_kingdom = {}\n",
+ "num_genera_kingdom = {}\n",
+ "num_species_kingdom = {}\n",
+ "for kingdom in df_taxa.kingdom.unique():\n",
+ " temp = df_taxa.loc[df_taxa.kingdom == kingdom]\n",
+ " num_families_kingdom[kingdom] = temp.family.nunique()\n",
+ " num_genera_kingdom[kingdom] = temp['genus'].nunique()\n",
+ " num_species_kingdom[kingdom] = temp['species'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{nan: 0,\n",
+ " 'Metazoa': 4272,\n",
+ " 'Archaeplastida': 719,\n",
+ " 'Fungi': 468,\n",
+ " 'Animalia': 1077,\n",
+ " 'Plantae': 286}"
+ ]
+ },
+ "execution_count": 14,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "num_families_kingdom"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Seems reasonable, let's get the larger of the higher class ones going, so check genus and species counts within families."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_genera_family = {}\n",
+ "num_species_family = {}\n",
+ "for family in df_taxa.family.unique():\n",
+ " temp = df_taxa.loc[df_taxa.family == family]\n",
+ " num_genera_family[family] = temp['genus'].nunique()\n",
+ " num_species_family[family] = temp['species'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Get counts for everything below order."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_families_order = {}\n",
+ "num_genera_order = {}\n",
+ "num_species_order = {}\n",
+ "for order in df_taxa.order.unique():\n",
+ " temp = df_taxa.loc[df_taxa.order == order]\n",
+ " num_families_order[order] = temp['family'].nunique()\n",
+ " num_genera_order[order] = temp['genus'].nunique()\n",
+ " num_species_order[order] = temp['species'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{nan: 0,\n",
+ " 'Lepidoptera': 128,\n",
+ " 'Sapindales': 9,\n",
+ " 'Trichoptera': 38,\n",
+ " 'Hemiptera': 135,\n",
+ " 'Coleoptera': 150,\n",
+ " 'Squamata': 54,\n",
+ " 'Tetraodontiformes': 10,\n",
+ " 'Mantodea': 31,\n",
+ " 'Heterobranchia': 43,\n",
+ " 'Lamiales': 24,\n",
+ " 'Fabales': 4,\n",
+ " 'Asterales': 10,\n",
+ " 'Carangiformes': 5,\n",
+ " 'Piperales': 3,\n",
+ " 'Caryophyllales': 39,\n",
+ " 'Boletales': 18,\n",
+ " 'Characiformes': 23,\n",
+ " 'Poales': 14,\n",
+ " 'Arecales': 2,\n",
+ " 'Malpighiales': 32,\n",
+ " 'Anura': 61,\n",
+ " 'Agaricales': 33,\n",
+ " 'Magnoliales': 5,\n",
+ " 'Hymenoptera': 101,\n",
+ " 'Littorinimorpha': 64,\n",
+ " 'Sessilia': 11,\n",
+ " 'Labriformes': 1,\n",
+ " 'Ricinulei': 1,\n",
+ " 'Helotiales': 18,\n",
+ " 'Asparagales': 13,\n",
+ " 'Proteales': 4,\n",
+ " 'Araneae': 111,\n",
+ " 'Polypodiales': 25,\n",
+ " 'Saurischia': 265,\n",
+ " 'Ulotrichales': 1,\n",
+ " 'Solanales': 5,\n",
+ " 'Diptera': 141,\n",
+ " 'Caudata': 9,\n",
+ " 'Saxifragales': 14,\n",
+ " 'Therapsida': 178,\n",
+ " 'Polyporales': 13,\n",
+ " 'Myrtales': 7,\n",
+ " 'Rosales': 8,\n",
+ " 'Decapoda': 78,\n",
+ " 'Phasmida': 13,\n",
+ " 'Imparidentia': 17,\n",
+ " 'Gobiiformes': 9,\n",
+ " 'Neogastropoda': 46,\n",
+ " 'Brassicales': 17,\n",
+ " 'Rhabdocoela': 32,\n",
+ " 'Cypriniformes': 275,\n",
+ " 'Orectolobiformes': 7,\n",
+ " 'Spariformes': 3,\n",
+ " 'Gentianales': 5,\n",
+ " 'Alismatales': 13,\n",
+ " 'Malvales': 11,\n",
+ " 'Pinales': 8,\n",
+ " 'Bryales': 13,\n",
+ " 'Nudipleura': 8,\n",
+ " 'Clupeiformes': 5,\n",
+ " 'Ericales': 21,\n",
+ " 'Chitonida': 12,\n",
+ " 'Apiales': 7,\n",
+ " 'Sebacinales': 1,\n",
+ " 'Lecanorales': 16,\n",
+ " 'Pertusariales': 4,\n",
+ " 'Commelinales': 5,\n",
+ " 'Orthoptera': 36,\n",
+ " 'Fagales': 7,\n",
+ " 'Dipsacales': 3,\n",
+ " 'Comatulida': 21,\n",
+ " 'Liliales': 11,\n",
+ " 'Monostilifera': 10,\n",
+ " 'Perciformes': 88,\n",
+ " 'Erysiphales': 1,\n",
+ " 'Ephippiformes': 2,\n",
+ " 'Carybdeida': 5,\n",
+ " 'Eurotiales': 3,\n",
+ " 'Odonata': 37,\n",
+ " 'Teloschistales': 3,\n",
+ " 'Russulales': 11,\n",
+ " 'Heteroscleromorpha': 17,\n",
+ " 'Polyzoniida': 3,\n",
+ " 'Stolidobranchia': 3,\n",
+ " 'Geraniales': 2,\n",
+ " 'Cyprinodontiformes': 10,\n",
+ " 'Chromadorea': 12,\n",
+ " 'Lophiiformes': 15,\n",
+ " 'Aquifoliales': 5,\n",
+ " 'Valvatacea': 3,\n",
+ " 'Gloeophyllales': 1,\n",
+ " 'Pezizales': 14,\n",
+ " 'Rhodymeniales': 6,\n",
+ " 'Neuroptera': 14,\n",
+ " 'Pteriomorphia': 12,\n",
+ " 'Trochida': 13,\n",
+ " 'Lutjanidae': 21,\n",
+ " 'Ranunculales': 7,\n",
+ " 'Salmoniformes': 1,\n",
+ " 'Megaloptera': 2,\n",
+ " 'Desmidiales': 4,\n",
+ " 'Octocorallia': 6,\n",
+ " 'Aulopiformes': 19,\n",
+ " 'Semaeostomeae': 5,\n",
+ " 'Ophiurida': 3,\n",
+ " 'Ixodida': 2,\n",
+ " 'Carcharhiniformes': 8,\n",
+ " 'Blattodea': 16,\n",
+ " 'Pandanales': 5,\n",
+ " 'Xylariales': 16,\n",
+ " 'Synallactida': 3,\n",
+ " 'Opiliones': 52,\n",
+ " 'Blenniiformes': 6,\n",
+ " 'Corticiales': 1,\n",
+ " 'Forcipulatacea': 2,\n",
+ " 'Kurtiformes': 2,\n",
+ " 'Syngnathiformes': 10,\n",
+ " 'Ephemeroptera': 25,\n",
+ " 'Bdelloidea': 4,\n",
+ " 'Orthotrichales': 2,\n",
+ " 'Hydroidolina': 9,\n",
+ " 'Santalales': 8,\n",
+ " 'Boraginales': 1,\n",
+ " 'Lycopodiales': 1,\n",
+ " 'Scleractinia': 26,\n",
+ " 'Siluriformes': 36,\n",
+ " 'Lepisosteiformes': 1,\n",
+ " 'Atheriniformes': 38,\n",
+ " 'Scombriformes': 16,\n",
+ " 'Gomphales': 3,\n",
+ " 'Testudines': 12,\n",
+ " 'Acanthuriformes': 3,\n",
+ " 'Carinacea': 4,\n",
+ " 'Gobiesociformes': 1,\n",
+ " 'Zingiberales': 8,\n",
+ " 'Pleuronectiformes': 13,\n",
+ " 'Microbotryales': 1,\n",
+ " 'Dermaptera': 8,\n",
+ " 'Capnodiales': 6,\n",
+ " 'Trentepohliales': 1,\n",
+ " 'Dicranales': 8,\n",
+ " 'Ulvales': 3,\n",
+ " 'Cycloneritida': 6,\n",
+ " 'Dilleniales': 1,\n",
+ " 'Hymenophyllales': 1,\n",
+ " 'Zygentoma': 2,\n",
+ " 'Nymphaeales': 3,\n",
+ " 'Phlebobranchia': 6,\n",
+ " 'Anguilliformes': 17,\n",
+ " 'Entomophaga': 0,\n",
+ " 'Pucciniales': 14,\n",
+ " 'Ceramiales': 7,\n",
+ " 'Isopoda': 49,\n",
+ " 'Holothuriida': 2,\n",
+ " 'Lichinales': 3,\n",
+ " 'Lepadiformes': 4,\n",
+ " 'Hypnales': 19,\n",
+ " 'Verongimorpha': 3,\n",
+ " 'Scorpiones': 15,\n",
+ " 'Actiniaria': 9,\n",
+ " 'Cichliformes': 2,\n",
+ " 'Marchantiidae': 3,\n",
+ " 'Laurales': 7,\n",
+ " 'Carditida': 4,\n",
+ " 'Cantharellales': 7,\n",
+ " 'Funariales': 6,\n",
+ " 'Tetraphidales': 2,\n",
+ " 'Raphidioptera': 2,\n",
+ " 'Palaeoheterodonta': 3,\n",
+ " 'Ploima': 20,\n",
+ " 'Plecoptera': 12,\n",
+ " 'Amphipoda': 51,\n",
+ " 'Marattiales': 1,\n",
+ " 'Cucurbitales': 8,\n",
+ " 'Haemulidae': 16,\n",
+ " 'Rhizostomeae': 3,\n",
+ " 'Embioptera': 8,\n",
+ " 'Harpacticoida': 32,\n",
+ " 'Rhynchobdellida': 2,\n",
+ " 'Chaetodontiformes': 2,\n",
+ " 'Oxalidales': 7,\n",
+ " 'Collothecacea': 2,\n",
+ " 'Salviniales': 2,\n",
+ " 'Tubeufiales': 1,\n",
+ " 'Seguenziida': 6,\n",
+ " 'Psilotales': 1,\n",
+ " 'Stauromedusae': 4,\n",
+ " 'Polydesmida': 16,\n",
+ " 'Halymeniales': 1,\n",
+ " 'Mecoptera': 7,\n",
+ " 'Laboulbeniales': 1,\n",
+ " 'Anabantiformes': 7,\n",
+ " 'Escalloniales': 1,\n",
+ " 'Rhizopodaceae': 1,\n",
+ " 'Hypocreales': 9,\n",
+ " 'Ophioglossales': 1,\n",
+ " 'Siphonaptera': 8,\n",
+ " 'Metzgeriidae': 2,\n",
+ " 'Beryciformes': 16,\n",
+ " 'Centrarchiformes': 24,\n",
+ " 'Selaginellales': 1,\n",
+ " 'Zygophyllales': 2,\n",
+ " 'Notostraca': 1,\n",
+ " 'Acoela': 16,\n",
+ " 'Squaliformes': 7,\n",
+ " 'Amphilepidida': 7,\n",
+ " 'Exobasidiales': 4,\n",
+ " 'Gigartinales': 26,\n",
+ " 'Celastrales': 2,\n",
+ " 'Acipenseriformes': 2,\n",
+ " 'Dasycladales': 2,\n",
+ " 'Gymnotiformes': 5,\n",
+ " 'Rajiformes': 3,\n",
+ " 'Diaporthales': 7,\n",
+ " 'Myliobatiformes': 9,\n",
+ " 'Geastrales': 1,\n",
+ " 'Phallales': 2,\n",
+ " 'Psocodea': 42,\n",
+ " 'Ephedrales': 1,\n",
+ " 'Gymnophiona': 9,\n",
+ " 'Spinulosacea': 1,\n",
+ " 'Jungermanniidae': 1,\n",
+ " 'Cheilostomatida': 60,\n",
+ " 'Lepetellida': 9,\n",
+ " 'Dioscoreales': 3,\n",
+ " 'Bruniales': 2,\n",
+ " 'Protobranchia': 5,\n",
+ " 'Rhytismatales': 4,\n",
+ " 'Candelariales': 1,\n",
+ " 'Cornales': 7,\n",
+ " 'Platydesmida': 1,\n",
+ " 'Peltigerales': 9,\n",
+ " 'Squatiniformes': 1,\n",
+ " 'Hymenochaetales': 4,\n",
+ " 'Cyatheales': 7,\n",
+ " 'Dictyoceratida': 4,\n",
+ " 'Irregularia': 4,\n",
+ " 'Seligeriaceae': 3,\n",
+ " 'Phyllodocida': 19,\n",
+ " 'Lamniformes': 6,\n",
+ " 'Auriculariales': 2,\n",
+ " 'Atelostomata': 7,\n",
+ " 'Calcinea': 1,\n",
+ " 'Calcaronea': 2,\n",
+ " 'Glomerellales': 2,\n",
+ " 'Leucodontaceae': 6,\n",
+ " 'Platyctenida': 2,\n",
+ " 'Crocodylia': 2,\n",
+ " 'Priacanthidae': 4,\n",
+ " 'Apodida': 3,\n",
+ " 'Architaenioglossa': 9,\n",
+ " 'Trombidiformes': 16,\n",
+ " 'Sordariales': 4,\n",
+ " 'Zoantharia': 7,\n",
+ " 'Icacinales': 1,\n",
+ " 'Cyclopoida': 35,\n",
+ " 'Gadiformes': 16,\n",
+ " 'Trachylinae': 3,\n",
+ " 'Tremellales': 6,\n",
+ " 'Enoplea': 6,\n",
+ " 'Cycadales': 2,\n",
+ " 'Myxiniformes': 1,\n",
+ " 'Stomatopoda': 3,\n",
+ " 'Charales': 1,\n",
+ " 'Furia': 0,\n",
+ " 'Beloniformes': 5,\n",
+ " 'Symphypleona': 6,\n",
+ " 'Uranoscopiformes': 4,\n",
+ " 'Octopoda': 13,\n",
+ " 'Amblypygi': 3,\n",
+ " 'Mycosphaerellaceae': 20,\n",
+ " 'Verrucariales': 1,\n",
+ " 'Sphaeropleales': 7,\n",
+ " 'Cidaroida': 4,\n",
+ " 'Arthoniales': 4,\n",
+ " 'Sphagnales': 1,\n",
+ " 'Entomobryomorpha': 4,\n",
+ " 'Petrosaviales': 1,\n",
+ " 'Osmundales': 1,\n",
+ " 'Thelephorales': 2,\n",
+ " 'Pleosporales': 24,\n",
+ " 'Bryopsidales': 6,\n",
+ " 'Plocamiales': 1,\n",
+ " 'Synbranchiformes': 4,\n",
+ " 'Mesostigmata': 6,\n",
+ " 'Julida': 6,\n",
+ " 'Chaetophorales': 2,\n",
+ " 'Pelliidae': 3,\n",
+ " 'Schizomida': 1,\n",
+ " 'Umbilicariales': 1,\n",
+ " 'Petromyzontiformes': 3,\n",
+ " 'Mycocaliciales': 2,\n",
+ " 'Dendrochirotida': 6,\n",
+ " 'Vitales': 1,\n",
+ " 'Monogenea': 5,\n",
+ " 'Gracilariales': 1,\n",
+ " 'Isoetales': 1,\n",
+ " 'Neolectales': 1,\n",
+ " 'Polypteriformes': 1,\n",
+ " 'Mugiliformes': 1,\n",
+ " 'Taphrinales': 1,\n",
+ " 'Equisetales': 1,\n",
+ " 'Patellariales': 1,\n",
+ " 'Tricladida': 9,\n",
+ " 'Botryosphaeriales': 3,\n",
+ " 'Pleurostigmophora': 4,\n",
+ " 'Ptilidiales': 2,\n",
+ " 'Austrobaileyales': 3,\n",
+ " 'Euryalida': 3,\n",
+ " 'Polycladida': 30,\n",
+ " 'Brachypoda': 1,\n",
+ " 'Grimmiales': 2,\n",
+ " 'Calanoida': 29,\n",
+ " 'Dolichomicrostomida': 2,\n",
+ " 'Ophiostomatales': 1,\n",
+ " 'Dacrymycetales': 1,\n",
+ " 'Holocentriformes': 1,\n",
+ " 'Xiphosurida': 1,\n",
+ " 'Gunnerales': 2,\n",
+ " 'Amphinomida': 2,\n",
+ " 'Pottiales': 3,\n",
+ " 'Phyllachorales': 2,\n",
+ " 'Gerreidae': 8,\n",
+ " 'Pantopoda': 10,\n",
+ " 'Argentiniformes': 4,\n",
+ " 'Prolecithophora': 5,\n",
+ " 'Pempheriformes': 16,\n",
+ " 'Polytrichales': 1,\n",
+ " 'Geoglossales': 1,\n",
+ " 'Mysida': 2,\n",
+ " 'Orbiliales': 1,\n",
+ " 'Trechisporales': 1,\n",
+ " 'Compsopogonales': 1,\n",
+ " 'Flosculariaceae': 5,\n",
+ " 'Chimaeriformes': 3,\n",
+ " 'Proseriata': 11,\n",
+ " 'Bangiophyceae': 3,\n",
+ " 'Onygenales': 4,\n",
+ " 'Amiiformes': 1,\n",
+ " 'Ustilaginales': 5,\n",
+ " 'Aplousobranchia': 10,\n",
+ " 'Porellales': 4,\n",
+ " 'Erythropeltidales': 2,\n",
+ " 'Hapalidiales': 1,\n",
+ " 'Tanaidacea': 4,\n",
+ " 'Salpida': 1,\n",
+ " 'Cestida': 1,\n",
+ " 'Climaciaceae': 1,\n",
+ " 'Alepocephaliformes': 2,\n",
+ " 'Gelidiales': 3,\n",
+ " 'Acarosporales': 1,\n",
+ " 'Hildenbrandiales': 1,\n",
+ " 'Ginkgoales': 1,\n",
+ " 'Ophiacanthida': 7,\n",
+ " 'Crassiclitellata': 10,\n",
+ " 'Phycomycetaceae': 2,\n",
+ " 'Ophioscolecida': 1,\n",
+ " 'Grylloblattodea': 1,\n",
+ " 'Pristiophoriformes': 1,\n",
+ " 'Crossosomatales': 4,\n",
+ " 'Heterodontiformes': 1,\n",
+ " 'Gigantorhynchida': 1,\n",
+ " 'Chlorellales': 2,\n",
+ " 'Baeomycetales': 3,\n",
+ " 'Phymatocerotales': 1,\n",
+ " 'Hedwigiaceae': 4,\n",
+ " 'Buxales': 1,\n",
+ " 'Trematoda': 9,\n",
+ " 'Sphaerotheriida': 4,\n",
+ " 'Ophidiiformes': 13,\n",
+ " 'Schizaeales': 3,\n",
+ " 'Antipatharia': 6,\n",
+ " 'Stomiiformes': 4,\n",
+ " 'Acroechinoidea': 3,\n",
+ " 'Molpadida': 3,\n",
+ " 'Sarcoptiformes': 43,\n",
+ " 'Gnetales': 1,\n",
+ " 'Pterobryaceae': 5,\n",
+ " 'Caproidae': 2,\n",
+ " 'Lampriformes': 6,\n",
+ " 'Scalpelliformes': 4,\n",
+ " 'Notostigmophora': 1,\n",
+ " 'Corallinales': 1,\n",
+ " 'Fissidentaceae': 1,\n",
+ " 'Halocyprida': 3,\n",
+ " 'Meteoriaceae': 5,\n",
+ " 'Osmeriformes': 4,\n",
+ " 'Galaxiiformes': 1,\n",
+ " 'Lingulata': 2,\n",
+ " 'Cestoda': 9,\n",
+ " 'Anostraca': 7,\n",
+ " 'Gleicheniales': 3,\n",
+ " 'Diplostraca': 14,\n",
+ " 'Cladophorales': 5,\n",
+ " 'Corallimorpharia': 3,\n",
+ " 'Trochodendrales': 1,\n",
+ " 'Poduromorpha': 5,\n",
+ " 'Ctenostomatida': 5,\n",
+ " 'Lobata': 4,\n",
+ " 'Acorales': 1,\n",
+ " 'Chordeumatida': 14,\n",
+ " 'Syzygites': 0,\n",
+ " 'Asterinales': 2,\n",
+ " 'Albuliformes': 1,\n",
+ " 'Hysteriales': 1,\n",
+ " 'Lophogastrida': 1,\n",
+ " 'Arhynchobdellida': 11,\n",
+ " 'Rhinopristiformes': 5,\n",
+ " 'Venturiales': 1,\n",
+ " 'Pleurotomariida': 1,\n",
+ " 'Torpediniformes': 5,\n",
+ " 'Amphisphaeriales': 5,\n",
+ " 'Canellales': 2,\n",
+ " 'Andreaeales': 1,\n",
+ " 'Palmariales': 4,\n",
+ " 'Chlamydomonadales': 8,\n",
+ " 'Entomophthora': 0,\n",
+ " 'Cyttariales': 1,\n",
+ " 'Elopiformes': 2,\n",
+ " 'Neckeraceae': 7,\n",
+ " 'Paracryphiales': 1,\n",
+ " 'Pseudoscorpiones': 14,\n",
+ " 'Urocystidales': 4,\n",
+ " 'Nanaloricida': 1,\n",
+ " 'Spirobolida': 10,\n",
+ " 'Coronatae': 6,\n",
+ " 'Myodocopida': 3,\n",
+ " 'Percopsiformes': 3,\n",
+ " 'Uropygi': 1,\n",
+ " 'Solifugae': 9,\n",
+ " 'Thysanoptera': 5,\n",
+ " 'Doassansiales': 2,\n",
+ " 'Garryales': 2,\n",
+ " 'Blasiidae': 1,\n",
+ " 'Eunicida': 5,\n",
+ " 'Hiodontiformes': 1,\n",
+ " 'Hysterangiales': 5,\n",
+ " 'Hookeriales': 2,\n",
+ " 'Beroida': 1,\n",
+ " 'Lyssacinosida': 3,\n",
+ " 'Notacanthiformes': 2,\n",
+ " 'Huerteales': 3,\n",
+ " 'Chaetosphaeriales': 1,\n",
+ " 'Cryphaeaceae': 1,\n",
+ " 'Lepidopleurida': 1,\n",
+ " 'Microascales': 3,\n",
+ " 'Fecampiida': 5,\n",
+ " 'Hyocrinida': 1,\n",
+ " 'Osteoglossiformes': 5,\n",
+ " 'Chaetothyriales': 2,\n",
+ " 'Ostropales': 7,\n",
+ " 'Helicobasidiales': 1,\n",
+ " 'Cepolidae': 3,\n",
+ " 'Entylomatales': 1,\n",
+ " 'Siphonostomatoida': 14,\n",
+ " 'Coniochaetales': 1,\n",
+ " 'Cystofilobasidiales': 1,\n",
+ " 'Istiophoriformes': 2,\n",
+ " 'Nautilida': 1,\n",
+ " 'Kickxellaceae': 3,\n",
+ " 'Neelipleona': 1,\n",
+ " 'Batrachoidiformes': 1,\n",
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+ " 'Dendroceratida': 2,\n",
+ " 'Ceriantharia': 2,\n",
+ " 'Cyclorhagida': 2,\n",
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+ " 'Myctophiformes': 2,\n",
+ " 'Pyrenulales': 2,\n",
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+ " 'Mytilinidiales': 2,\n",
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+ " 'Polymorphida': 1,\n",
+ " 'Nemastomatales': 2,\n",
+ " 'Palmophyllales': 1,\n",
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+ " 'Mucoraceae': 7,\n",
+ " 'Coronophorales': 3,\n",
+ " 'Nemaliales': 3,\n",
+ " 'Spirostreptida': 6,\n",
+ " 'Euphausiacea': 2,\n",
+ " 'Phomatospora': 0,\n",
+ " 'Rhynchonellata': 4,\n",
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+ " 'Copelata': 2,\n",
+ " 'Trachichthyiformes': 5,\n",
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+ " 'Boliniales': 1,\n",
+ " 'Zygnematales': 2,\n",
+ " 'Archaeognatha': 2,\n",
+ " 'Saccharomycetales': 5,\n",
+ " 'Phragmophora': 1,\n",
+ " 'Ornithischia': 9,\n",
+ " 'Tremellodendropsidaceae': 1,\n",
+ " 'Hexanchiformes': 2,\n",
+ " 'Massospora': 0,\n",
+ " 'Cyclostomatida': 6,\n",
+ " 'Triblidiales': 1,\n",
+ " 'Callipodida': 4,\n",
+ " 'Strepsiptera': 4,\n",
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+ " 'Gonorynchiformes': 3,\n",
+ " 'Chloranthales': 1,\n",
+ " 'Ceratodontiformes': 3,\n",
+ " 'Tetrasporales': 2,\n",
+ " 'Pilobolaceae': 1,\n",
+ " 'Anthocerotales': 1,\n",
+ " 'Porocephalida': 2,\n",
+ " 'Macrodasyida': 7,\n",
+ " 'Lobotiformes': 3,\n",
+ " 'Gadilida': 2,\n",
+ " 'Buxbaumiales': 1,\n",
+ " 'Isocrinida': 3,\n",
+ " 'Isobryales': 4,\n",
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+ " 'Dentaliida': 7,\n",
+ " 'Ceratophyllales': 1,\n",
+ " 'Myriangiales': 2,\n",
+ " 'Pyrosomatida': 1,\n",
+ " 'Sceptrulophora': 4,\n",
+ " 'Euechinoidea': 1,\n",
+ " 'Gordioidea': 2,\n",
+ " 'Parachela': 4,\n",
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+ " 'Branchiobdellida': 2,\n",
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+ " 'Thelebolales': 1,\n",
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+ " 'Chaetonotida': 2,\n",
+ " 'Oligacanthorhynchida': 1,\n",
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+ " 'Stereopsis': 0,\n",
+ " 'Amylocorticiales': 1,\n",
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+ " 'Enchytraeida': 1,\n",
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+ " 'Coryneliales': 1,\n",
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+ " 'Schistostegaceae': 1,\n",
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+ " 'Geminibasidiaceae': 2,\n",
+ " 'Leptodontaceae': 1,\n",
+ " 'Echinorhynchida': 3,\n",
+ " 'Batrachospermales': 2,\n",
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+ " 'Amphioxiformes': 1,\n",
+ " 'Septobasidiales': 1,\n",
+ " 'Monstrilloida': 1,\n",
+ " 'Thalassocalycida': 1,\n",
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+ " 'Stylonematales': 1,\n",
+ " 'Mormonilloida': 1,\n",
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+ " 'Vampyromorpha': 1,\n",
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+ " 'Canuelloida': 2,\n",
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+ " 'Glaucocystales': 1,\n",
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+ " 'Lichenoconiales': 1,\n",
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+ " 'Zoophthora': 0,\n",
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+ " 'Trypetheliales': 2,\n",
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+ " 'Acrospermales': 1,\n",
+ " 'Magnaporthales': 2,\n",
+ " 'Bothrioplanida': 1,\n",
+ " 'Ahnfeltiales': 1,\n",
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+ " 'Endogonaceae': 1,\n",
+ " 'Archidiales': 1,\n",
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+ " 'Opilioacarida': 1,\n",
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+ " 'Echiniscoidea': 1,\n",
+ " 'Melanosporales': 1,\n",
+ " 'Microthyriales': 1,\n",
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+ " 'Eryniopsis': 0,\n",
+ " 'Malasseziales': 1,\n",
+ " 'Schizosaccharomycetales': 1,\n",
+ " 'Microstromatales': 0,\n",
+ " 'Pyramimonadophyceae': 0,\n",
+ " 'Glomus': 0,\n",
+ " 'Doliolida': 1,\n",
+ " 'Acrosymphytales': 2,\n",
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+ " 'Jobellisiaceae': 1,\n",
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+ " 'Coelacanthiformes': 1,\n",
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+ " 'Cunninghamellaceae': 3,\n",
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+ " 'Meliolales': 1,\n",
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+ " 'Klebsormidiales': 1,\n",
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+ " 'Rhodochaetales': 1,\n",
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+ " 'Phacopida': 3,\n",
+ " 'Rhizophagus': 0,\n",
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+ " 'Sebdeniales': 1,\n",
+ " 'Multivalvulida': 1,\n",
+ " 'Stylephoriformes': 1,\n",
+ " 'Zoraptera': 1,\n",
+ " 'Symbiida': 1,\n",
+ " 'Coleochaetales': 1,\n",
+ " 'Arthrotardigrada': 1,\n",
+ " 'Sporidiobolales': 0,\n",
+ " 'Tilletiales': 1,\n",
+ " 'Bursovaginoidea': 1,\n",
+ " 'Chaetodermatida': 2,\n",
+ " 'Mycotyphaceae': 1,\n",
+ " 'Tryblidiida': 1,\n",
+ " 'Cryptophialida': 1,\n",
+ " 'Chlorodendrales': 1,\n",
+ " 'Mesostigmatales': 1,\n",
+ " 'Geosiphon': 0,\n",
+ " 'Misophrioida': 1,\n",
+ " 'Scutellospora': 0,\n",
+ " 'Sporodiniella': 0,\n",
+ " 'Gnosonesimidae': 1,\n",
+ " 'Corynexochida': 1,\n",
+ " 'Hypnobryales': 1,\n",
+ " 'Redeckera': 0,\n",
+ " 'Oedogoniales': 0,\n",
+ " 'Lepidogalaxiiformes': 1,\n",
+ " 'Peripodida': 1,\n",
+ " 'Thoreales': 1,\n",
+ " 'Passeriformes': 72,\n",
+ " 'Columbiformes': 1,\n",
+ " 'Anseriformes': 3,\n",
+ " 'Accipitriformes': 3,\n",
+ " 'Nudibranchia': 16,\n",
+ " 'Adapedonta': 1,\n",
+ " 'Charadriiformes': 11,\n",
+ " 'Pelecaniformes': 4,\n",
+ " 'Piciformes': 4,\n",
+ " 'Sphenisciformes': 1,\n",
+ " 'Mytilida': 1,\n",
+ " 'Suliformes': 4,\n",
+ " 'Gruiformes': 3,\n",
+ " 'Scolopendromorpha': 1,\n",
+ " 'Rhodellales': 1,\n",
+ " 'Carnivora': 10,\n",
+ " 'Primates': 3,\n",
+ " 'Phoenicopteriformes': 1,\n",
+ " 'Strigiformes': 2,\n",
+ " 'Chiroptera': 4,\n",
+ " 'Artiodactyla': 12,\n",
+ " 'Ciconiiformes': 1,\n",
+ " 'Galliformes': 5,\n",
+ " 'Lagomorpha': 2,\n",
+ " 'Cuculiformes': 1,\n",
+ " 'Coraciiformes': 4,\n",
+ " 'Stylommatophora': 20,\n",
+ " 'Colaconematales': 1,\n",
+ " 'Venerida': 3,\n",
+ " 'Pectinida': 2,\n",
+ " 'Psittaciformes': 4,\n",
+ " 'Rodentia': 11,\n",
+ " 'Camarodonta': 2,\n",
+ " 'Procellariiformes': 2,\n",
+ " 'Forcipulatida': 1,\n",
+ " 'Caprimulgiformes': 5,\n",
+ " 'Marchantiales': 3,\n",
+ " 'Galbuliformes': 1,\n",
+ " 'Eulipotyphla': 3,\n",
+ " 'Myida': 3,\n",
+ " 'Falconiformes': 1,\n",
+ " 'Perissodactyla': 3,\n",
+ " 'Pilosa': 3,\n",
+ " 'Lecideales': 1,\n",
+ " 'Podicipediformes': 1,\n",
+ " 'Phaeotrichales': 1,\n",
+ " 'Scorpaeniformes': 3,\n",
+ " 'Ostreida': 1,\n",
+ " 'Sepiida': 1,\n",
+ " 'Caliciales': 1,\n",
+ " 'Trogoniformes': 1,\n",
+ " 'Cyrtocrinida': 1,\n",
+ " 'Dimargaritaceae': 1,\n",
+ " 'Cingulata': 1,\n",
+ " 'Casuariiformes': 1,\n",
+ " 'Diprotodontia': 5,\n",
+ " 'Rhynchocephalia': 1,\n",
+ " 'Endeostigmata': 1,\n",
+ " 'Jahnulales': 1,\n",
+ " 'Filospermoidea': 1,\n",
+ " 'Otidiformes': 1,\n",
+ " 'Cathartiformes': 1,\n",
+ " 'Spirulida': 1,\n",
+ " 'Bucerotiformes': 4,\n",
+ " 'Opisthocomiformes': 1,\n",
+ " 'Gaviiformes': 1,\n",
+ " 'Agaricostilbales': 0,\n",
+ " 'Monotremata': 2,\n",
+ " 'Gasterosteiformes': 1,\n",
+ " 'Sabellida': 2,\n",
+ " 'Coliiformes': 1,\n",
+ " 'Phacidiales': 1,\n",
+ " 'Jungermanniales': 1,\n",
+ " 'Sirenia': 1,\n",
+ " 'Aplysiida': 1,\n",
+ " 'Spinulosida': 1,\n",
+ " 'Musophagiformes': 1,\n",
+ " 'Cardiida': 2,\n",
+ " 'Didelphimorphia': 1,\n",
+ " 'Systellommatophora': 1,\n",
+ " 'Unionida': 1,\n",
+ " 'Scutigeromorpha': 1,\n",
+ " 'Clypeasteroida': 2,\n",
+ " 'Anthoathecata': 1,\n",
+ " 'Siphonophorae': 1,\n",
+ " 'Cephalaspidea': 1,\n",
+ " 'Haplotaxida': 1,\n",
+ " 'Lunulariales': 1,\n",
+ " 'Valvatida': 3,\n",
+ " 'Hyracoidea': 1,\n",
+ " 'Proboscidea': 1,\n",
+ " 'Dermoptera': 1,\n",
+ " 'Struthioniformes': 1,\n",
+ " 'Craniata': 1,\n",
+ " 'Rhizocarpales': 1,\n",
+ " 'Hedwigiales': 1}"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "num_families_order"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_orders_class = {}\n",
+ "num_families_class = {}\n",
+ "num_genera_class = {}\n",
+ "num_species_class = {}\n",
+ "for clss in df_taxa['class'].unique():\n",
+ " temp = df_taxa.loc[df_taxa['class'] == clss]\n",
+ " num_orders_class[clss] = temp['order'].nunique()\n",
+ " num_families_class[clss] = temp['family'].nunique()\n",
+ " num_genera_class[clss] = temp['genus'].nunique()\n",
+ " num_species_class[clss] = temp['species'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_classes_phylum = {}\n",
+ "num_orders_phylum = {}\n",
+ "num_families_phylum = {}\n",
+ "num_genera_phylum = {}\n",
+ "num_species_phylum = {}\n",
+ "for phylum in df_taxa.phylum.unique():\n",
+ " temp = df_taxa.loc[df_taxa.phylum == phylum]\n",
+ " num_classes_phylum[phylum] = temp['class'].nunique()\n",
+ " num_orders_phylum[phylum] = temp['order'].nunique()\n",
+ " num_families_phylum[phylum] = temp['family'].nunique()\n",
+ " num_genera_phylum[phylum] = temp['genus'].nunique()\n",
+ " num_species_phylum[phylum] = temp['species'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_phyla_kingdom = {}\n",
+ "num_classes_kingdom = {}\n",
+ "num_orders_kingdom = {}\n",
+ "for kingdom in df_taxa.kingdom.unique():\n",
+ " temp = df_taxa.loc[df_taxa.kingdom == kingdom]\n",
+ " num_phyla_kingdom[kingdom] = temp.phylum.nunique()\n",
+ " num_classes_kingdom[kingdom] = temp['class'].nunique()\n",
+ " num_orders_kingdom[kingdom] = temp['order'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 49,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "num_species_genus = {}\n",
+ "for genus in df_taxa.genus.unique():\n",
+ " temp = df_taxa.loc[df_taxa.genus == genus]\n",
+ " num_species_genus[genus] = temp.species.nunique()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Quick pause to save all progress to csv before starting final long calculation, then we can just add the number of species in each genus at the end."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#### Compile list of dictionaries to make DataFrame with all data\n",
+ "\n",
+ "Format:\n",
+ "| top_taxon | rank | num_phyla | num_classes | num_orders | num_families | num_genera | num_species |\n",
+ "| ------ | ------ | ---- | ---- | ---- | ---- | ---- | ---- |\n",
+ "| Animalia | Kingdom | # phyla | # classes | # orders | # families | # genera | # species |\n",
+ "..."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "kingdom_counts = [num_phyla_kingdom, num_classes_kingdom, num_orders_kingdom, num_families_kingdom, \n",
+ " num_genera_kingdom, num_species_kingdom]\n",
+ "phylum_counts = [num_classes_phylum, num_orders_phylum, num_families_phylum, num_genera_phylum, num_species_phylum]\n",
+ "class_counts = [num_orders_class, num_families_class, num_genera_class, num_species_class]\n",
+ "order_counts = [num_families_order, num_genera_order, num_species_order]\n",
+ "family_counts = [num_genera_family, num_species_family]\n",
+ "genus_counts = [num_species_genus]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "dict_list = [{\"kingdom\": kingdom_counts},\n",
+ " {\"phylum\": phylum_counts},\n",
+ " {\"class\": class_counts},\n",
+ " {\"order\": order_counts},\n",
+ " {\"family\": family_counts},\n",
+ " {\"genus\": genus_counts}]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Generate the first two columns of our desired DataFrame. Note that all taxa but `genus` start with `nan` so we will ignore that value --not in first iteration"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "top_taxon = []\n",
+ "ranks = []\n",
+ "#i = 1\n",
+ "for taxon in taxa[:6]:\n",
+ " vals = list(df_taxa[taxon].unique())\n",
+ " #if taxon == 'genus': # since genus is last in list\n",
+ " # i = 0\n",
+ " for val in vals: #[i:]:\n",
+ " top_taxon.append(val)\n",
+ " ranks.append(taxon)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "taxa_cols = ['num_phyla', 'num_classes', 'num_orders', 'num_families', 'num_genera', 'num_species']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "taxa_counts_df = pd.DataFrame({\"top_taxon\": top_taxon, \"rank\": ranks})"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " top_taxon | \n",
+ " rank | \n",
+ " num_phyla | \n",
+ " num_classes | \n",
+ " num_orders | \n",
+ " num_families | \n",
+ " num_genera | \n",
+ " num_species | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " | 0 | \n",
+ " NaN | \n",
+ " kingdom | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 1 | \n",
+ " Metazoa | \n",
+ " kingdom | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 2 | \n",
+ " Archaeplastida | \n",
+ " kingdom | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 3 | \n",
+ " Fungi | \n",
+ " kingdom | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 4 | \n",
+ " Animalia | \n",
+ " kingdom | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " | 96536 | \n",
+ " Kribia | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96537 | \n",
+ " Chilodonta | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96538 | \n",
+ " Epihippus | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96539 | \n",
+ " Ancistria | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96540 | \n",
+ " Exneria | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
96541 rows × 8 columns
\n",
+ "
"
+ ],
+ "text/plain": [
+ " top_taxon rank num_phyla num_classes num_orders \\\n",
+ "0 NaN kingdom 1 1 1 \n",
+ "1 Metazoa kingdom 1 1 1 \n",
+ "2 Archaeplastida kingdom 1 1 1 \n",
+ "3 Fungi kingdom 1 1 1 \n",
+ "4 Animalia kingdom 1 1 1 \n",
+ "... ... ... ... ... ... \n",
+ "96536 Kribia genus 1 1 1 \n",
+ "96537 Chilodonta genus 1 1 1 \n",
+ "96538 Epihippus genus 1 1 1 \n",
+ "96539 Ancistria genus 1 1 1 \n",
+ "96540 Exneria genus 1 1 1 \n",
+ "\n",
+ " num_families num_genera num_species \n",
+ "0 1 1 1 \n",
+ "1 1 1 1 \n",
+ "2 1 1 1 \n",
+ "3 1 1 1 \n",
+ "4 1 1 1 \n",
+ "... ... ... ... \n",
+ "96536 1 1 1 \n",
+ "96537 1 1 1 \n",
+ "96538 1 1 1 \n",
+ "96539 1 1 1 \n",
+ "96540 1 1 1 \n",
+ "\n",
+ "[96541 rows x 8 columns]"
+ ]
+ },
+ "execution_count": 27,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# Set all other columns to default value of 1 since lower level taxa will only belong to the one higher level taxon\n",
+ "taxa_counts_df[taxa_cols] = 1\n",
+ "taxa_counts_df"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 34,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "nan 0\n",
+ "0\n",
+ "Metazoa 31\n",
+ "0\n",
+ "Archaeplastida 7\n",
+ "0\n",
+ "Fungi 11\n",
+ "0\n",
+ "Animalia 6\n",
+ "0\n",
+ "Plantae 5\n",
+ "0\n",
+ "nan 0\n",
+ "1\n",
+ "Metazoa 61\n",
+ "1\n",
+ "Archaeplastida 22\n",
+ "1\n",
+ "Fungi 36\n",
+ "1\n",
+ "Animalia 27\n",
+ "1\n",
+ "Plantae 14\n",
+ "1\n",
+ "nan 0\n",
+ "2\n",
+ "Metazoa 355\n",
+ "2\n",
+ "Archaeplastida 176\n",
+ "2\n",
+ "Fungi 152\n",
+ "2\n",
+ "Animalia 160\n",
+ "2\n",
+ "Plantae 85\n",
+ "2\n",
+ "nan 0\n",
+ "3\n",
+ "Metazoa 4272\n",
+ "3\n",
+ "Archaeplastida 719\n",
+ "3\n",
+ "Fungi 468\n",
+ "3\n",
+ "Animalia 1077\n",
+ "3\n",
+ "Plantae 286\n",
+ "3\n",
+ "nan 0\n",
+ "4\n",
+ "Metazoa 39686\n",
+ "4\n",
+ "Archaeplastida 10182\n",
+ "4\n",
+ "Fungi 2019\n",
+ "4\n",
+ "Animalia 6225\n",
+ "4\n",
+ "Plantae 1702\n",
+ "4\n",
+ "nan 0\n",
+ "5\n",
+ "Metazoa 74323\n",
+ "5\n",
+ "Archaeplastida 33054\n",
+ "5\n",
+ "Fungi 7713\n",
+ "5\n",
+ "Animalia 12476\n",
+ "5\n",
+ "Plantae 2499\n",
+ "5\n"
+ ]
+ }
+ ],
+ "source": [
+ "marker = 0\n",
+ "for king_dict in kingdom_counts:\n",
+ " for key, value in king_dict.items():\n",
+ " # key = higher taxon, value = num of lower taxa in it\n",
+ " print(key, value)\n",
+ " print(marker)\n",
+ " taxa_counts_df.loc[(taxa_counts_df['top_taxon'] == key) & (taxa_counts_df['rank'] == 'kingdom'), taxa_cols[marker]] = value\n",
+ " marker += 1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 35,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " top_taxon | \n",
+ " rank | \n",
+ " num_phyla | \n",
+ " num_classes | \n",
+ " num_orders | \n",
+ " num_families | \n",
+ " num_genera | \n",
+ " num_species | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " | 0 | \n",
+ " NaN | \n",
+ " kingdom | \n",
+ " 1 | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 1 | \n",
+ " Metazoa | \n",
+ " kingdom | \n",
+ " 31 | \n",
+ " 61 | \n",
+ " 355 | \n",
+ " 4272 | \n",
+ " 39686 | \n",
+ " 74323 | \n",
+ "
\n",
+ " \n",
+ " | 2 | \n",
+ " Archaeplastida | \n",
+ " kingdom | \n",
+ " 7 | \n",
+ " 22 | \n",
+ " 176 | \n",
+ " 719 | \n",
+ " 10182 | \n",
+ " 33054 | \n",
+ "
\n",
+ " \n",
+ " | 3 | \n",
+ " Fungi | \n",
+ " kingdom | \n",
+ " 11 | \n",
+ " 36 | \n",
+ " 152 | \n",
+ " 468 | \n",
+ " 2019 | \n",
+ " 7713 | \n",
+ "
\n",
+ " \n",
+ " | 4 | \n",
+ " Animalia | \n",
+ " kingdom | \n",
+ " 6 | \n",
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+ " 160 | \n",
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+ " 6225 | \n",
+ " 12476 | \n",
+ "
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+ " \n",
+ " | ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " | 96536 | \n",
+ " Kribia | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96537 | \n",
+ " Chilodonta | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96538 | \n",
+ " Epihippus | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96539 | \n",
+ " Ancistria | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96540 | \n",
+ " Exneria | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
96541 rows × 8 columns
\n",
+ "
"
+ ],
+ "text/plain": [
+ " top_taxon rank num_phyla num_classes num_orders \\\n",
+ "0 NaN kingdom 1 1 1 \n",
+ "1 Metazoa kingdom 31 61 355 \n",
+ "2 Archaeplastida kingdom 7 22 176 \n",
+ "3 Fungi kingdom 11 36 152 \n",
+ "4 Animalia kingdom 6 27 160 \n",
+ "... ... ... ... ... ... \n",
+ "96536 Kribia genus 1 1 1 \n",
+ "96537 Chilodonta genus 1 1 1 \n",
+ "96538 Epihippus genus 1 1 1 \n",
+ "96539 Ancistria genus 1 1 1 \n",
+ "96540 Exneria genus 1 1 1 \n",
+ "\n",
+ " num_families num_genera num_species \n",
+ "0 1 1 1 \n",
+ "1 4272 39686 74323 \n",
+ "2 719 10182 33054 \n",
+ "3 468 2019 7713 \n",
+ "4 1077 6225 12476 \n",
+ "... ... ... ... \n",
+ "96536 1 1 1 \n",
+ "96537 1 1 1 \n",
+ "96538 1 1 1 \n",
+ "96539 1 1 1 \n",
+ "96540 1 1 1 \n",
+ "\n",
+ "[96541 rows x 8 columns]"
+ ]
+ },
+ "execution_count": 35,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa_counts_df"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "marker = 1\n",
+ "for phylum_dict in phylum_counts:\n",
+ " for key, value in phylum_dict.items():\n",
+ " # key = higher taxon, value = num of lower taxa in it\n",
+ " taxa_counts_df.loc[(taxa_counts_df['top_taxon'] == key) & (taxa_counts_df['rank'] == 'phylum'), taxa_cols[marker]] = value\n",
+ " marker += 1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 38,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
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+ " num_phyla | \n",
+ " num_classes | \n",
+ " num_orders | \n",
+ " num_families | \n",
+ " num_genera | \n",
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+ "
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+ " \n",
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+ " \n",
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+ " 4272 | \n",
+ " 39686 | \n",
+ " 74323 | \n",
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\n",
+ " \n",
+ " | 2 | \n",
+ " Archaeplastida | \n",
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+ " 7 | \n",
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+ " 176 | \n",
+ " 719 | \n",
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+ " \n",
+ " | 5 | \n",
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+ " 2499 | \n",
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\n",
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+ " 60992 | \n",
+ "
\n",
+ " \n",
+ " | 8 | \n",
+ " Tracheophyta | \n",
+ " phylum | \n",
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+ " 9 | \n",
+ " 81 | \n",
+ " 463 | \n",
+ " 9418 | \n",
+ " 32622 | \n",
+ "
\n",
+ " \n",
+ " | 9 | \n",
+ " Chordata | \n",
+ " phylum | \n",
+ " 1 | \n",
+ " 13 | \n",
+ " 158 | \n",
+ " 1551 | \n",
+ " 7762 | \n",
+ " 20969 | \n",
+ "
\n",
+ " \n",
+ "
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+ "
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+ ],
+ "text/plain": [
+ " top_taxon rank num_phyla num_classes num_orders num_families \\\n",
+ "0 NaN kingdom 1 1 1 1 \n",
+ "1 Metazoa kingdom 31 61 355 4272 \n",
+ "2 Archaeplastida kingdom 7 22 176 719 \n",
+ "3 Fungi kingdom 11 36 152 468 \n",
+ "4 Animalia kingdom 6 27 160 1077 \n",
+ "5 Plantae kingdom 5 14 85 286 \n",
+ "6 NaN phylum 1 1 1 1 \n",
+ "7 Arthropoda phylum 1 13 108 1747 \n",
+ "8 Tracheophyta phylum 1 9 81 463 \n",
+ "9 Chordata phylum 1 13 158 1551 \n",
+ "\n",
+ " num_genera num_species \n",
+ "0 1 1 \n",
+ "1 39686 74323 \n",
+ "2 10182 33054 \n",
+ "3 2019 7713 \n",
+ "4 6225 12476 \n",
+ "5 1702 2499 \n",
+ "6 1 1 \n",
+ "7 28515 60992 \n",
+ "8 9418 32622 \n",
+ "9 7762 20969 "
+ ]
+ },
+ "execution_count": 38,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa_counts_df.head(10)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 39,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "marker = 2\n",
+ "for class_dict in class_counts:\n",
+ " for key, value in class_dict.items():\n",
+ " # key = higher taxon, value = num of lower taxa in it\n",
+ " taxa_counts_df.loc[(taxa_counts_df['top_taxon'] == key) & (taxa_counts_df['rank'] == 'class'), taxa_cols[marker]] = value\n",
+ " marker += 1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 40,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " top_taxon | \n",
+ " rank | \n",
+ " num_phyla | \n",
+ " num_classes | \n",
+ " num_orders | \n",
+ " num_families | \n",
+ " num_genera | \n",
+ " num_species | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " | 56 | \n",
+ " NaN | \n",
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+ " \n",
+ " | 57 | \n",
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+ " 68 | \n",
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+ " 24878 | \n",
+ " 49513 | \n",
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\n",
+ " \n",
+ " | 58 | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 96 | \n",
+ " 1504 | \n",
+ " 7521 | \n",
+ " 20133 | \n",
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\n",
+ " \n",
+ " | 59 | \n",
+ " Gastropoda | \n",
+ " class | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 15 | \n",
+ " 301 | \n",
+ " 2214 | \n",
+ " 7699 | \n",
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\n",
+ " \n",
+ " | 60 | \n",
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+ " class | \n",
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+ " ... | \n",
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+ " ... | \n",
+ "
\n",
+ " \n",
+ " | 188 | \n",
+ " Gnetopsida | \n",
+ " class | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 2 | \n",
+ "
\n",
+ " \n",
+ " | 189 | \n",
+ " Polychaeta | \n",
+ " class | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 2 | \n",
+ " 3 | \n",
+ " 3 | \n",
+ "
\n",
+ " \n",
+ " | 190 | \n",
+ " Cycadopsida | \n",
+ " class | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 191 | \n",
+ " Clitellata | \n",
+ " class | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 192 | \n",
+ " Craniiformea | \n",
+ " class | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 0 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
137 rows × 8 columns
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+ "
"
+ ],
+ "text/plain": [
+ " top_taxon rank num_phyla num_classes num_orders num_families \\\n",
+ "56 NaN class 1 1 1 1 \n",
+ "57 Pancrustacea class 1 1 68 1276 \n",
+ "58 Gnathostomata class 1 1 96 1504 \n",
+ "59 Gastropoda class 1 1 15 301 \n",
+ "60 Agaricomycetes class 1 1 20 108 \n",
+ ".. ... ... ... ... ... ... \n",
+ "188 Gnetopsida class 1 1 1 1 \n",
+ "189 Polychaeta class 1 1 1 2 \n",
+ "190 Cycadopsida class 1 1 1 1 \n",
+ "191 Clitellata class 1 1 1 1 \n",
+ "192 Craniiformea class 1 1 1 1 \n",
+ "\n",
+ " num_genera num_species \n",
+ "56 1 1 \n",
+ "57 24878 49513 \n",
+ "58 7521 20133 \n",
+ "59 2214 7699 \n",
+ "60 776 4900 \n",
+ ".. ... ... \n",
+ "188 1 2 \n",
+ "189 3 3 \n",
+ "190 1 1 \n",
+ "191 1 1 \n",
+ "192 1 0 \n",
+ "\n",
+ "[137 rows x 8 columns]"
+ ]
+ },
+ "execution_count": 40,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa_counts_df.loc[taxa_counts_df['rank'] == 'class']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 41,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "marker = 3\n",
+ "for order_dict in order_counts:\n",
+ " for key, value in order_dict.items():\n",
+ " # key = higher taxon, value = num of lower taxa in it\n",
+ " taxa_counts_df.loc[(taxa_counts_df['top_taxon'] == key) & (taxa_counts_df['rank'] == 'order'), taxa_cols[marker]] = value\n",
+ " marker += 1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 42,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
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+ " \n",
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+ " num_phyla | \n",
+ " num_classes | \n",
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+ " num_genera | \n",
+ " num_species | \n",
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+ " \n",
+ " \n",
+ " \n",
+ " | 193 | \n",
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+ " 1 | \n",
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+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 194 | \n",
+ " Lepidoptera | \n",
+ " order | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 128 | \n",
+ " 7599 | \n",
+ " 25071 | \n",
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\n",
+ " \n",
+ " | 195 | \n",
+ " Sapindales | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 9 | \n",
+ " 310 | \n",
+ " 1362 | \n",
+ "
\n",
+ " \n",
+ " | 196 | \n",
+ " Trichoptera | \n",
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+ " 1 | \n",
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+ " 38 | \n",
+ " 253 | \n",
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+ " | 197 | \n",
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+ " 6144 | \n",
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+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " | 955 | \n",
+ " Dermoptera | \n",
+ " order | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 956 | \n",
+ " Struthioniformes | \n",
+ " order | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 957 | \n",
+ " Craniata | \n",
+ " order | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 0 | \n",
+ "
\n",
+ " \n",
+ " | 958 | \n",
+ " Rhizocarpales | \n",
+ " order | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 959 | \n",
+ " Hedwigiales | \n",
+ " order | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
767 rows × 8 columns
\n",
+ "
"
+ ],
+ "text/plain": [
+ " top_taxon rank num_phyla num_classes num_orders \\\n",
+ "193 NaN order 1 1 1 \n",
+ "194 Lepidoptera order 1 1 1 \n",
+ "195 Sapindales order 1 1 1 \n",
+ "196 Trichoptera order 1 1 1 \n",
+ "197 Hemiptera order 1 1 1 \n",
+ ".. ... ... ... ... ... \n",
+ "955 Dermoptera order 1 1 1 \n",
+ "956 Struthioniformes order 1 1 1 \n",
+ "957 Craniata order 1 1 1 \n",
+ "958 Rhizocarpales order 1 1 1 \n",
+ "959 Hedwigiales order 1 1 1 \n",
+ "\n",
+ " num_families num_genera num_species \n",
+ "193 1 1 1 \n",
+ "194 128 7599 25071 \n",
+ "195 9 310 1362 \n",
+ "196 38 253 1056 \n",
+ "197 135 3290 6144 \n",
+ ".. ... ... ... \n",
+ "955 1 1 1 \n",
+ "956 1 1 1 \n",
+ "957 1 1 0 \n",
+ "958 1 1 1 \n",
+ "959 1 1 1 \n",
+ "\n",
+ "[767 rows x 8 columns]"
+ ]
+ },
+ "execution_count": 42,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa_counts_df.loc[taxa_counts_df['rank'] == 'order']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 43,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "marker = 4\n",
+ "for family_dict in family_counts:\n",
+ " for key, value in family_dict.items():\n",
+ " # key = higher taxon, value = num of lower taxa in it\n",
+ " taxa_counts_df.loc[(taxa_counts_df['top_taxon'] == key) & (taxa_counts_df['rank'] == 'family'), taxa_cols[marker]] = value\n",
+ " marker += 1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 44,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
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\n",
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\n",
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+ " ... | \n",
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\n",
+ " \n",
+ " | 6621 | \n",
+ " Hedwigiaceae | \n",
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+ " 1 | \n",
+ " 1 | \n",
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\n",
+ " \n",
+ " | 6622 | \n",
+ " Jasmineiricolidae | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
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\n",
+ " \n",
+ " | 6623 | \n",
+ " Cunninghamella | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 0 | \n",
+ " 0 | \n",
+ "
\n",
+ " \n",
+ " | 6624 | \n",
+ " Eremobelbidae | \n",
+ " family | \n",
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+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
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\n",
+ " \n",
+ " | 6625 | \n",
+ " Rhopalomeniidae | \n",
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+ " 1 | \n",
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\n",
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+ "
\n",
+ "
5666 rows × 8 columns
\n",
+ "
"
+ ],
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+ "960 NaN family 1 1 1 \n",
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+ "962 Rutaceae family 1 1 1 \n",
+ "963 Limnephilidae family 1 1 1 \n",
+ "964 Reduviidae family 1 1 1 \n",
+ "... ... ... ... ... ... \n",
+ "6621 Hedwigiaceae family 1 1 1 \n",
+ "6622 Jasmineiricolidae family 1 1 1 \n",
+ "6623 Cunninghamella family 1 1 1 \n",
+ "6624 Eremobelbidae family 1 1 1 \n",
+ "6625 Rhopalomeniidae family 1 1 1 \n",
+ "\n",
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+ "960 1 1 1 \n",
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+ "6624 1 1 1 \n",
+ "6625 1 1 1 \n",
+ "\n",
+ "[5666 rows x 8 columns]"
+ ]
+ },
+ "execution_count": 44,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa_counts_df.loc[taxa_counts_df['rank'] == 'family']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 45,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "marker = 5\n",
+ "for genus_dict in genus_counts:\n",
+ " for key, value in genus_dict.items():\n",
+ " # key = higher taxon, value = num of lower taxa in it\n",
+ " taxa_counts_df.loc[(taxa_counts_df['top_taxon'] == key) & (taxa_counts_df['rank'] == 'genus'), taxa_cols[marker]] = value\n",
+ " marker += 1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 46,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " top_taxon | \n",
+ " rank | \n",
+ " num_phyla | \n",
+ " num_classes | \n",
+ " num_orders | \n",
+ " num_families | \n",
+ " num_genera | \n",
+ " num_species | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " | 6626 | \n",
+ " Manfreda | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 3 | \n",
+ "
\n",
+ " \n",
+ " | 6627 | \n",
+ " Discophlebia | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 5 | \n",
+ "
\n",
+ " \n",
+ " | 6628 | \n",
+ " Melicope | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 39 | \n",
+ "
\n",
+ " \n",
+ " | 6629 | \n",
+ " Limnephilus | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 81 | \n",
+ "
\n",
+ " \n",
+ " | 6630 | \n",
+ " NaN | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " | 96536 | \n",
+ " Kribia | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96537 | \n",
+ " Chilodonta | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96538 | \n",
+ " Epihippus | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96539 | \n",
+ " Ancistria | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ " | 96540 | \n",
+ " Exneria | \n",
+ " genus | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ " 1 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
89915 rows × 8 columns
\n",
+ "
"
+ ],
+ "text/plain": [
+ " top_taxon rank num_phyla num_classes num_orders num_families \\\n",
+ "6626 Manfreda genus 1 1 1 1 \n",
+ "6627 Discophlebia genus 1 1 1 1 \n",
+ "6628 Melicope genus 1 1 1 1 \n",
+ "6629 Limnephilus genus 1 1 1 1 \n",
+ "6630 NaN genus 1 1 1 1 \n",
+ "... ... ... ... ... ... ... \n",
+ "96536 Kribia genus 1 1 1 1 \n",
+ "96537 Chilodonta genus 1 1 1 1 \n",
+ "96538 Epihippus genus 1 1 1 1 \n",
+ "96539 Ancistria genus 1 1 1 1 \n",
+ "96540 Exneria genus 1 1 1 1 \n",
+ "\n",
+ " num_genera num_species \n",
+ "6626 1 3 \n",
+ "6627 1 5 \n",
+ "6628 1 39 \n",
+ "6629 1 81 \n",
+ "6630 1 1 \n",
+ "... ... ... \n",
+ "96536 1 1 \n",
+ "96537 1 1 \n",
+ "96538 1 1 \n",
+ "96539 1 1 \n",
+ "96540 1 1 \n",
+ "\n",
+ "[89915 rows x 8 columns]"
+ ]
+ },
+ "execution_count": 46,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "taxa_counts_df.loc[taxa_counts_df['rank'] == 'genus']"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Save resulting DataFrame to CSV. Note that the number of species per genus did not finish."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 48,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "taxa_counts_df.to_csv(\"../data/taxa_counts.csv\", index = False)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Returning to our original DataFrame, we want to get some counts by source dataset."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Add data_source column for easier slicing\n",
+ "df.loc[df['inat21_filename'].notna(), 'data_source'] = 'iNat21'\n",
+ "df.loc[df['bioscan_filename'].notna(), 'data_source'] = 'BIOSCAN'\n",
+ "df.loc[df['eol_content_id'].notna(), 'data_source'] = 'EOL'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "518118"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df.loc[df['data_source'] == 'EOL', 'common'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "9941"
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df.loc[df['data_source'] == 'iNat21', 'common'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "10635"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df.loc[df['data_source'] == 'BIOSCAN', 'common'].nunique()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "viz",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.10"
+ },
+ "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}