"Adding"

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

bren-meds213-spring-2024-class-data.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

week3/.ipynb_checkpoints/pandas-checkpoint.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "a74b4cb1-722b-4e09-b511-7cd3e5b4a4cc",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Defaulting to user installation because normal site-packages is not writeable\n",
+      "Requirement already satisfied: duckdb in /Users/dmnavarro/.local/lib/python3.7/site-packages (0.10.2)\n",
+      "\n",
+      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n",
+      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
+   "source": [
+    "%pip install duckdb"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "14680f2b-7b7e-4cc2-8515-6b258c30fc73",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import duckdb"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "fee61f08-59ba-4570-a45d-f2869088687b",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "conn = duckdb.connect(\"database.db\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "cc5496dd-ad10-487b-a0fa-17b5e90d38c3",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "cur = conn.cursor()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "75bdd2f4-5216-453c-bddb-dad8b108ea3c",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[(2005,\n",
+       "  'bylo',\n",
+       "  'lmckinnon',\n",
+       "  datetime.date(2005, 6, 1),\n",
+       "  datetime.date(2005, 8, 5)),\n",
+       " (2005,\n",
+       "  'bylo',\n",
+       "  'blalibert',\n",
+       "  datetime.date(2005, 6, 1),\n",
+       "  datetime.date(2005, 8, 20)),\n",
+       " (2006,\n",
+       "  'bylo',\n",
+       "  'lmckinnon',\n",
+       "  datetime.date(2006, 6, 1),\n",
+       "  datetime.date(2006, 8, 5))]"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cur.execute(\"SELECT * FROM Camp_assignment LIMIT 3\")\n",
+    "cur.fetchall()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "064ae9ac-cca5-46db-bbd5-6f6cb4b225e3",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[]"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cur.fetchall()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "029c7e65-ea39-4c59-a0b4-ec5e4c8405c7",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "cur.fetchone()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "ebfbe6a2-046e-47a3-bd34-db2141b5a1a2",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Observer dkessler gathered 69 nests\n",
+      "Observer bharrington gathered 245 nests\n",
+      "Observer lmckinnon gathered 249 nests\n",
+      "Observer dhodkinson gathered 15 nests\n",
+      "Observer bhill gathered 55 nests\n",
+      "Observer ssaalfeld gathered 13 nests\n",
+      "Observer wenglish gathered 18 nests\n",
+      "Observer lworing gathered 14 nests\n",
+      "Observer vloverti gathered 54 nests\n",
+      "Observer rlanctot gathered 40 nests\n",
+      "Observer abankert gathered 17 nests\n",
+      "Observer edastrous gathered 38 nests\n",
+      "Observer amould gathered 42 nests\n",
+      "Observer bkaselow gathered 4 nests\n",
+      "Observer jflamarre gathered 43 nests\n",
+      "Observer jzamuido gathered 11 nests\n",
+      "Observer mballvanzee gathered 2 nests\n",
+      "Observer mbwunder gathered 4 nests\n",
+      "Observer None gathered 0 nests\n",
+      "Observer kkalasz gathered 12 nests\n"
+     ]
+    }
+   ],
+   "source": [
+    "inner_query = \"\"\"\n",
+    "    SELECT COUNT(*) AS num_nests \n",
+    "    FROM Bird_nests\n",
+    "    WHERE Observer = ?\n",
+    "\"\"\"\n",
+    "\n",
+    "outer_query = \"\"\"\n",
+    "    SELECT DISTINCT Observer FROM Bird_nests \n",
+    "\"\"\"\n",
+    "\n",
+    "for row in cur.execute(outer_query).fetchall():\n",
+    "    observer = row[0]\n",
+    "    cur2 = conn.cursor()\n",
+    "    cur2.execute(inner_query, [observer])\n",
+    "    print(f\"Observer {observer} gathered {cur2.fetchone()[0]} nests\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7fc40ac6-5763-4c8d-a4f1-5005e14adc8c",
+   "metadata": {},
+   "source": [
+    "Pandas"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "50cd90c9-59ba-431d-9a16-8210b289e003",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "e5f7d7b6-24a9-4b3a-9697-fceb0e267360",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "df = pd.read_sql(\"SELECT * FROM Site\", conn)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7c87eb5e-9c76-45e5-9503-9a80bcea69de",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    " "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.7.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}