{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Way number eight of looking at the correlation coefficient\n", "\n", "This is a notebook to accompany the blog post [\"Way number eight of looking at the correlation coefficient\"](http://composition.al/blog/2019/01/31/way-number-eight-of-looking-at-the-correlation-coefficient/). Read the post for additional context!" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "from datascience import *\n", "from datetime import *\n", "import matplotlib\n", "%matplotlib inline\n", "import matplotlib.pyplot as plots\n", "from mpl_toolkits.mplot3d import Axes3D\n", "import pandas as pd\n", "import math" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Recap from last time\n", "\n", "As [before](http://composition.al/blog/2018/08/31/understanding-the-regression-line-with-standard-units/), we're using the [datascience](http://data8.org/datascience/) package, and everything else we're using is pretty standard.\n", "\n", "And, as before, here's the data we'll be working with, [converted to standard units](https://www.inferentialthinking.com/chapters/14/2/Variability#standard-units) and plotted:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Date Height (standard units) Weight (standard units)
07/28/2017 -1.26135 -1.3158
08/07/2017 -1.08691 -1.13054
08/25/2017 -0.912464 -0.808628
09/25/2017 -0.228116 -0.399485
11/28/2017 0.107349 0.254728
01/26/2018 0.617255 0.728253
04/27/2018 1.12716 1.2537
07/30/2018 1.63707 1.41777
" ], "text/plain": [ "Date | Height (standard units) | Weight (standard units)\n", "07/28/2017 | -1.26135 | -1.3158\n", "08/07/2017 | -1.08691 | -1.13054\n", "08/25/2017 | -0.912464 | -0.808628\n", "09/25/2017 | -0.228116 | -0.399485\n", "11/28/2017 | 0.107349 | 0.254728\n", "01/26/2018 | 0.617255 | 0.728253\n", "04/27/2018 | 1.12716 | 1.2537\n", "07/30/2018 | 1.63707 | 1.41777" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "heightweight = Table().with_columns([\n", " 'Date', ['07/28/2017', '08/07/2017', '08/25/2017', '09/25/2017', '11/28/2017', '01/26/2018', '04/27/2018', '07/30/2018'],\n", " 'Height (cm)', [ 53.3, 54.6, 55.9, 61, 63.5, 67.3, 71.1, 74.9],\n", " 'Weight (kg)', [ 4.204, 4.65, 5.425, 6.41, 7.985, 9.125, 10.39, 10.785],\n", " ])\n", "def standard_units(nums):\n", " return (nums - np.mean(nums)) / np.std(nums)\n", "\n", "heightweight_standard = Table().with_columns(\n", " 'Date', heightweight.column('Date'),\n", " 'Height (standard units)', standard_units(heightweight.column('Height (cm)')),\n", " 'Weight (standard units)', standard_units(heightweight.column('Weight (kg)')))\n", "heightweight_standard" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "image/png": 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "heightweight_standard.scatter(\n", " 'Height (standard units)',\n", " 'Weight (standard units)')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Visualizing the data in \"person space\"\n", "\n", "So far, this is all a recap of [last time](http://composition.al/blog/2018/08/31/understanding-the-regression-line-with-standard-units/). Now, let's try turning our data sideways.\n", "\n", "The hacky way I have of doing this is to convert the data first to a numpy [ndarray](https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html), then to a [pandas DataFrame](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html), and then [transposing](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.T.html#pandas.DataFrame.T) the DataFrame. This is kind of silly, but I don't know a better way to transpose a [structured ndarray](https://docs.scipy.org/doc/numpy/user/basics.rec.html). If you do, let me know." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Date07/28/201708/07/201708/25/201709/25/201711/28/201701/26/201804/27/201807/30/2018
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" ], "text/plain": [ " 0 1 2 3 \\\n", "Date 07/28/2017 08/07/2017 08/25/2017 09/25/2017 \n", "Height (standard units) -1.26135 -1.08691 -0.912464 -0.228116 \n", "Weight (standard units) -1.3158 -1.13054 -0.808628 -0.399485 \n", "\n", " 4 5 6 7 \n", "Date 11/28/2017 01/26/2018 04/27/2018 07/30/2018 \n", "Height (standard units) 0.107349 0.617255 1.12716 1.63707 \n", "Weight (standard units) 0.254728 0.728253 1.2537 1.41777 " ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# First convert to a plain old numpy ndarray.\n", "heightweight_standard_np = heightweight_standard.to_array()\n", "\n", "# Now convert *that* to a pandas DataFrame.\n", "df = pd.DataFrame(heightweight_standard_np)\n", "\n", "# Get the transpose of the DataFrame.\n", "df = df.T\n", "df" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "pandas defaults to using `RangeIndex (0, 1, 2, …, n)` for the column labels, but we want the dates from the first row to be the column headers rather than being an actual row. That's [an easy change to make](https://stackoverflow.com/questions/26147180/convert-row-to-column-header-for-pandas-dataframe), though." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Date07/28/201708/07/201708/25/201709/25/201711/28/201701/26/201804/27/201807/30/2018
Height (standard units)-1.26135-1.08691-0.912464-0.2281160.1073490.6172551.127161.63707
Weight (standard units)-1.3158-1.13054-0.808628-0.3994850.2547280.7282531.25371.41777
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" ], "text/plain": [ "Date 07/28/2017 08/07/2017 08/25/2017 09/25/2017 \\\n", "Height (standard units) -1.26135 -1.08691 -0.912464 -0.228116 \n", "Weight (standard units) -1.3158 -1.13054 -0.808628 -0.399485 \n", "\n", "Date 11/28/2017 01/26/2018 04/27/2018 07/30/2018 \n", "Height (standard units) 0.107349 0.617255 1.12716 1.63707 \n", "Weight (standard units) 0.254728 0.728253 1.2537 1.41777 " ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df.columns = df.iloc[0]\n", "df = df.drop(\"Date\")\n", "df" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "While we're at it, we'll convert the values in our DataFrame to numeric values, so that we can visualize them in a moment." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Date07/28/201708/07/201708/25/201709/25/201711/28/201701/26/201804/27/201807/30/2018
Height (standard units)-1.261347-1.086906-0.912464-0.2281160.1073490.6172551.1271611.637068
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" ], "text/plain": [ "Date 07/28/2017 08/07/2017 08/25/2017 09/25/2017 \\\n", "Height (standard units) -1.261347 -1.086906 -0.912464 -0.228116 \n", "Weight (standard units) -1.315798 -1.130542 -0.808628 -0.399485 \n", "\n", "Date 11/28/2017 01/26/2018 04/27/2018 07/30/2018 \n", "Height (standard units) 0.107349 0.617255 1.127161 1.637068 \n", "Weight (standard units) 0.254728 0.728253 1.253700 1.417773 " ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = df.apply(pd.to_numeric)\n", "df" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Eight dimensions are too many to try to visualize, but we can pare it down to three. We'll pick three -- the first (07/28/2017), the last (07/30/2018), and one in the middle (01/26/2018) -- and drop the rest." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Date07/28/201701/26/201807/30/2018
Height (standard units)-1.2613470.6172551.637068
Weight (standard units)-1.3157980.7282531.417773
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" ], "text/plain": [ "Date 07/28/2017 01/26/2018 07/30/2018\n", "Height (standard units) -1.261347 0.617255 1.637068\n", "Weight (standard units) -1.315798 0.728253 1.417773" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df_3dim = df.drop(df.columns[[1, 2, 3, 4, 6]],axis=1)\n", "df_3dim" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we can visualize the data with a three-dimensional scatter plot." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
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