{ "cells": [ { "cell_type": "markdown", "id": "202599bf", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Transformations and diagnostics\n", "\n", "Peter Ralph\n", "\n", "https://uodsci.github.io/dsci345" ] }, { "cell_type": "code", "execution_count": 2, "id": "733bfdf0", "metadata": { "slideshow": { "slide_type": "skip" } }, "outputs": [], "source": [ "import matplotlib\n", "import matplotlib.pyplot as plt\n", "matplotlib.rcParams['figure.figsize'] = (15, 8)\n", "import numpy as np\n", "import pandas as pd\n", "from dsci345 import pretty\n", "\n", "rng = np.random.default_rng()" ] }, { "cell_type": "markdown", "id": "88ec5c59", "metadata": { "slideshow": { "slide_type": "skip" } }, "source": [ "$$\\renewcommand{\\P}{\\mathbb{P}} \\newcommand{\\E}{\\mathbb{E}} \\newcommand{\\var}{\\text{var}} \\newcommand{\\sd}{\\text{sd}} \\newcommand{\\cov}{\\text{cov}} \\newcommand{\\cor}{\\text{cor}}$$\n", "This is here so we can use `\\P` and `\\E` and `\\var` and `\\cov` and `\\cor` and `\\sd` in LaTeX below." ] }, { "cell_type": "markdown", "id": "79439dd2", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# An example" ] }, { "cell_type": "markdown", "id": "b6e3b2b4", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "Let's look at how newborn (i.e., \"neonate\") body mass\n", "is related to adult body mass,\n", "across a bunch of mammal species\n", "(in the order Carnivora, including dogs, cats, bears, weasels, and seals). [(data link)](https://github.com/UOdsci/dsci345/blob/main/class_material/slides/data/carnivora_sizes.csv)" ] }, { "cell_type": "code", "execution_count": 3, "id": "97f0423c", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | Family | \n", "NeonateBodyMass_g | \n", "AdultBodyMass_g | \n", "AgeatEyeOpening_d | \n", "WeaningAge_d | \n", "
---|---|---|---|---|---|
Binomial | \n", "\n", " | \n", " | \n", " | \n", " | \n", " |
Canis aureus | \n", "Canidae | \n", "211.82 | \n", "9658.70 | \n", "7.50 | \n", "61.30 | \n", "
Canis latrans | \n", "Canidae | \n", "200.01 | \n", "11989.10 | \n", "11.94 | \n", "43.71 | \n", "
Canis lupus | \n", "Canidae | \n", "412.31 | \n", "31756.51 | \n", "14.01 | \n", "44.82 | \n", "
Canis mesomelas | \n", "Canidae | \n", "177.20 | \n", "8247.30 | \n", "NaN | \n", "34.10 | \n", "
Callorhinus ursinus | \n", "Otariidae | \n", "5354.80 | \n", "55464.82 | \n", "0.00 | \n", "108.69 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
Vulpes lagopus | \n", "Canidae | \n", "69.17 | \n", "3584.37 | \n", "15.03 | \n", "49.50 | \n", "
Vulpes velox | \n", "Canidae | \n", "39.94 | \n", "2088.00 | \n", "12.50 | \n", "47.08 | \n", "
Vulpes vulpes | \n", "Canidae | \n", "100.49 | \n", "4820.36 | \n", "14.01 | \n", "50.71 | \n", "
Vulpes zerda | \n", "Canidae | \n", "28.04 | \n", "1317.13 | \n", "16.95 | \n", "65.56 | \n", "
Zalophus californianus | \n", "Otariidae | \n", "6347.89 | \n", "137194.86 | \n", "0.00 | \n", "319.01 | \n", "
145 rows × 5 columns
\n", "\n", " | Family | \n", "NeonateBodyMass_g | \n", "AdultBodyMass_g | \n", "AgeatEyeOpening_d | \n", "WeaningAge_d | \n", "PredictedNeonateMass | \n", "residual | \n", "
---|---|---|---|---|---|---|---|
Binomial | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
Canis aureus | \n", "Canidae | \n", "211.82 | \n", "9658.70 | \n", "7.50 | \n", "61.30 | \n", "916.205446 | \n", "-704.385446 | \n", "
Canis latrans | \n", "Canidae | \n", "200.01 | \n", "11989.10 | \n", "11.94 | \n", "43.71 | \n", "1003.630922 | \n", "-803.620922 | \n", "
Canis lupus | \n", "Canidae | \n", "412.31 | \n", "31756.51 | \n", "14.01 | \n", "44.82 | \n", "1745.209715 | \n", "-1332.899715 | \n", "
Canis mesomelas | \n", "Canidae | \n", "177.20 | \n", "8247.30 | \n", "NaN | \n", "34.10 | \n", "863.256460 | \n", "-686.056460 | \n", "
Callorhinus ursinus | \n", "Otariidae | \n", "5354.80 | \n", "55464.82 | \n", "0.00 | \n", "108.69 | \n", "2634.632251 | \n", "2720.167749 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
Vulpes lagopus | \n", "Canidae | \n", "69.17 | \n", "3584.37 | \n", "15.03 | \n", "49.50 | \n", "688.325602 | \n", "-619.155602 | \n", "
Vulpes velox | \n", "Canidae | \n", "39.94 | \n", "2088.00 | \n", "12.50 | \n", "47.08 | \n", "632.188948 | \n", "-592.248948 | \n", "
Vulpes vulpes | \n", "Canidae | \n", "100.49 | \n", "4820.36 | \n", "14.01 | \n", "50.71 | \n", "734.694042 | \n", "-634.204042 | \n", "
Vulpes zerda | \n", "Canidae | \n", "28.04 | \n", "1317.13 | \n", "16.95 | \n", "65.56 | \n", "603.269588 | \n", "-575.229588 | \n", "
Zalophus californianus | \n", "Otariidae | \n", "6347.89 | \n", "137194.86 | \n", "0.00 | \n", "319.01 | \n", "5700.752923 | \n", "647.137077 | \n", "
145 rows × 7 columns
\n", "\n", " | Family | \n", "NeonateBodyMass_g | \n", "AdultBodyMass_g | \n", "AgeatEyeOpening_d | \n", "WeaningAge_d | \n", "PredictedNeonateMass | \n", "residual | \n", "logAdultBodyMass_g | \n", "logNeonateBodyMass_g | \n", "
---|---|---|---|---|---|---|---|---|---|
Binomial | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
Canis aureus | \n", "Canidae | \n", "211.82 | \n", "9658.70 | \n", "7.50 | \n", "61.30 | \n", "916.205446 | \n", "-704.385446 | \n", "9.175614 | \n", "5.355737 | \n", "
Canis latrans | \n", "Canidae | \n", "200.01 | \n", "11989.10 | \n", "11.94 | \n", "43.71 | \n", "1003.630922 | \n", "-803.620922 | \n", "9.391753 | \n", "5.298367 | \n", "
Canis lupus | \n", "Canidae | \n", "412.31 | \n", "31756.51 | \n", "14.01 | \n", "44.82 | \n", "1745.209715 | \n", "-1332.899715 | \n", "10.365853 | \n", "6.021775 | \n", "
Canis mesomelas | \n", "Canidae | \n", "177.20 | \n", "8247.30 | \n", "NaN | \n", "34.10 | \n", "863.256460 | \n", "-686.056460 | \n", "9.017641 | \n", "5.177279 | \n", "
Callorhinus ursinus | \n", "Otariidae | \n", "5354.80 | \n", "55464.82 | \n", "0.00 | \n", "108.69 | \n", "2634.632251 | \n", "2720.167749 | \n", "10.923504 | \n", "8.585749 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
Vulpes lagopus | \n", "Canidae | \n", "69.17 | \n", "3584.37 | \n", "15.03 | \n", "49.50 | \n", "688.325602 | \n", "-619.155602 | \n", "8.184338 | \n", "4.236567 | \n", "
Vulpes velox | \n", "Canidae | \n", "39.94 | \n", "2088.00 | \n", "12.50 | \n", "47.08 | \n", "632.188948 | \n", "-592.248948 | \n", "7.643962 | \n", "3.687378 | \n", "
Vulpes vulpes | \n", "Canidae | \n", "100.49 | \n", "4820.36 | \n", "14.01 | \n", "50.71 | \n", "734.694042 | \n", "-634.204042 | \n", "8.480604 | \n", "4.610058 | \n", "
Vulpes zerda | \n", "Canidae | \n", "28.04 | \n", "1317.13 | \n", "16.95 | \n", "65.56 | \n", "603.269588 | \n", "-575.229588 | \n", "7.183210 | \n", "3.333632 | \n", "
Zalophus californianus | \n", "Otariidae | \n", "6347.89 | \n", "137194.86 | \n", "0.00 | \n", "319.01 | \n", "5700.752923 | \n", "647.137077 | \n", "11.829158 | \n", "8.755878 | \n", "
145 rows × 9 columns
\n", "