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| { | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "# Create Table One" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "The `CreateTableOne()` function from the `tableone` package is a handy tool to get an overview of your data while allowing stratification (i.e. grouping)\n", | |
| "based on certrain categorical variables. Lets have a look at the `mtcars` data set and stratify by transmssion type (`am`: 0 = automatic, 1 = manual) and engine type (`vs`: 0 = V-shaped, 1 = straight)." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 21, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "library(tableone)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 22, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 3 × 11</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>mpg</th><th scope=col>cyl</th><th scope=col>disp</th><th scope=col>hp</th><th scope=col>drat</th><th scope=col>wt</th><th scope=col>qsec</th><th scope=col>vs</th><th scope=col>am</th><th scope=col>gear</th><th scope=col>carb</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>Mazda RX4</th><td>21.0</td><td>6</td><td>160</td><td>110</td><td>3.90</td><td>2.620</td><td>16.46</td><td>0</td><td>1</td><td>4</td><td>4</td></tr>\n", | |
| "\t<tr><th scope=row>Mazda RX4 Wag</th><td>21.0</td><td>6</td><td>160</td><td>110</td><td>3.90</td><td>2.875</td><td>17.02</td><td>0</td><td>1</td><td>4</td><td>4</td></tr>\n", | |
| "\t<tr><th scope=row>Datsun 710</th><td>22.8</td><td>4</td><td>108</td><td> 93</td><td>3.85</td><td>2.320</td><td>18.61</td><td>1</td><td>1</td><td>4</td><td>1</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 3 × 11\n", | |
| "\\begin{tabular}{r|lllllllllll}\n", | |
| " & mpg & cyl & disp & hp & drat & wt & qsec & vs & am & gear & carb\\\\\n", | |
| " & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl>\\\\\n", | |
| "\\hline\n", | |
| "\tMazda RX4 & 21.0 & 6 & 160 & 110 & 3.90 & 2.620 & 16.46 & 0 & 1 & 4 & 4\\\\\n", | |
| "\tMazda RX4 Wag & 21.0 & 6 & 160 & 110 & 3.90 & 2.875 & 17.02 & 0 & 1 & 4 & 4\\\\\n", | |
| "\tDatsun 710 & 22.8 & 4 & 108 & 93 & 3.85 & 2.320 & 18.61 & 1 & 1 & 4 & 1\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 3 × 11\n", | |
| "\n", | |
| "| <!--/--> | mpg <dbl> | cyl <dbl> | disp <dbl> | hp <dbl> | drat <dbl> | wt <dbl> | qsec <dbl> | vs <dbl> | am <dbl> | gear <dbl> | carb <dbl> |\n", | |
| "|---|---|---|---|---|---|---|---|---|---|---|---|\n", | |
| "| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 | 16.46 | 0 | 1 | 4 | 4 |\n", | |
| "| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 | 17.02 | 0 | 1 | 4 | 4 |\n", | |
| "| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 | 18.61 | 1 | 1 | 4 | 1 |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " mpg cyl disp hp drat wt qsec vs am gear carb\n", | |
| "Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 \n", | |
| "Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 \n", | |
| "Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# show the mtcars structure\n", | |
| "head(mtcars, n = 3)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 23, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "vars <- c(\"mpg\", \"cyl\", \"disp\", \"hp\", \"drat\", \"wt\", \"qsec\", \"gear\", \"carb\")\n", | |
| "# specify stratification variables\n", | |
| "strata <- c(\"am\", \"vs\")\n", | |
| "# specify categorical variables\n", | |
| "cat_vars <- c(\"cyl\", \"gear\", \"carb\")" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 24, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| " Stratified by am:vs\n", | |
| " 0:0 1:0 0:1 1:1 \n", | |
| " n 12 6 7 7 \n", | |
| " mpg (mean (SD)) 15.05 (2.77) 19.75 (4.01) 20.74 (2.47) 28.37 (4.76) \n", | |
| " cyl (%) \n", | |
| " 4 0 ( 0.0) 1 (16.7) 3 (42.9) 7 (100.0) \n", | |
| " 6 0 ( 0.0) 3 (50.0) 4 (57.1) 0 ( 0.0) \n", | |
| " 8 12 (100.0) 2 (33.3) 0 ( 0.0) 0 ( 0.0) \n", | |
| " disp (mean (SD)) 357.62 (71.82) 206.22 (95.23) 175.11 (49.13) 89.80 (18.80) \n", | |
| " hp (mean (SD)) 194.17 (33.36) 180.83 (98.82) 102.14 (20.93) 80.57 (24.14) \n", | |
| " drat (mean (SD)) 3.12 (0.23) 3.94 (0.34) 3.57 (0.46) 4.15 (0.38) \n", | |
| " wt (mean (SD)) 4.10 (0.77) 2.86 (0.49) 3.19 (0.35) 2.03 (0.44) \n", | |
| " qsec (mean (SD)) 17.14 (0.80) 15.80 (1.09) 19.97 (1.46) 18.70 (0.95) \n", | |
| " gear (%) \n", | |
| " 3 12 (100.0) 0 ( 0.0) 3 (42.9) 0 ( 0.0) \n", | |
| " 4 0 ( 0.0) 2 (33.3) 4 (57.1) 6 ( 85.7) \n", | |
| " 5 0 ( 0.0) 4 (66.7) 0 ( 0.0) 1 ( 14.3) \n", | |
| " carb (%) \n", | |
| " 1 0 ( 0.0) 0 ( 0.0) 3 (42.9) 4 ( 57.1) \n", | |
| " 2 4 ( 33.3) 1 (16.7) 2 (28.6) 3 ( 42.9) \n", | |
| " 3 3 ( 25.0) 0 ( 0.0) 0 ( 0.0) 0 ( 0.0) \n", | |
| " 4 5 ( 41.7) 3 (50.0) 2 (28.6) 0 ( 0.0) \n", | |
| " 6 0 ( 0.0) 1 (16.7) 0 ( 0.0) 0 ( 0.0) \n", | |
| " 8 0 ( 0.0) 1 (16.7) 0 ( 0.0) 0 ( 0.0) " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# CreateTableOne\n", | |
| "CreateTableOne(data = mtcars, vars = vars, strata = strata,\n", | |
| " factorVars = cat_vars, test = FALSE)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "## From this summary table you can draw preliminary conclusions such as:\n", | |
| "* cars with automatic transmission and V-shaped engines exhibit the lowest milage per gallon (`mpg`)\n", | |
| "* cars with straight engines and manual transmission are likely designed to have less cylinders (`cyl`)\n", | |
| "* the fastest cars on the quarter mile speed test (`qsec`) have a manual transmission and a V-shaped motor" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "## Assume you would like the have the median an IQR displayed for the horsepower (`hp`) and weight (`wt`)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "For this you need to adjust the print options `TableOne` object. Please note that the table is wrapped into two \"lines\" because of the size of the returned table." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 25, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| " Stratified by am:vs\n", | |
| " 0:0 1:0 \n", | |
| " n 12 6 \n", | |
| " mpg (mean (SD)) 15.05 (2.77) 19.75 (4.01) \n", | |
| " cyl (%) \n", | |
| " 4 0 ( 0.0) 1 (16.7) \n", | |
| " 6 0 ( 0.0) 3 (50.0) \n", | |
| " 8 12 (100.0) 2 (33.3) \n", | |
| " disp (mean (SD)) 357.62 (71.82) 206.22 (95.23) \n", | |
| " hp (median [IQR]) 180.00 [175.00, 218.75] 142.50 [110.00, 241.75]\n", | |
| " drat (mean (SD)) 3.12 (0.23) 3.94 (0.34) \n", | |
| " wt (median [IQR]) 3.81 [3.56, 4.37] 2.82 [2.66, 3.10] \n", | |
| " qsec (mean (SD)) 17.14 (0.80) 15.80 (1.09) \n", | |
| " gear (%) \n", | |
| " 3 12 (100.0) 0 ( 0.0) \n", | |
| " 4 0 ( 0.0) 2 (33.3) \n", | |
| " 5 0 ( 0.0) 4 (66.7) \n", | |
| " carb (%) \n", | |
| " 1 0 ( 0.0) 0 ( 0.0) \n", | |
| " 2 4 ( 33.3) 1 (16.7) \n", | |
| " 3 3 ( 25.0) 0 ( 0.0) \n", | |
| " 4 5 ( 41.7) 3 (50.0) \n", | |
| " 6 0 ( 0.0) 1 (16.7) \n", | |
| " 8 0 ( 0.0) 1 (16.7) \n", | |
| " Stratified by am:vs\n", | |
| " 0:1 1:1 \n", | |
| " n 7 7 \n", | |
| " mpg (mean (SD)) 20.74 (2.47) 28.37 (4.76) \n", | |
| " cyl (%) \n", | |
| " 4 3 (42.9) 7 (100.0) \n", | |
| " 6 4 (57.1) 0 ( 0.0) \n", | |
| " 8 0 ( 0.0) 0 ( 0.0) \n", | |
| " disp (mean (SD)) 175.11 (49.13) 89.80 (18.80) \n", | |
| " hp (median [IQR]) 105.00 [96.00, 116.50] 66.00 [65.50, 101.00]\n", | |
| " drat (mean (SD)) 3.57 (0.46) 4.15 (0.38) \n", | |
| " wt (median [IQR]) 3.21 [3.17, 3.44] 1.94 [1.73, 2.26] \n", | |
| " qsec (mean (SD)) 19.97 (1.46) 18.70 (0.95) \n", | |
| " gear (%) \n", | |
| " 3 3 (42.9) 0 ( 0.0) \n", | |
| " 4 4 (57.1) 6 ( 85.7) \n", | |
| " 5 0 ( 0.0) 1 ( 14.3) \n", | |
| " carb (%) \n", | |
| " 1 3 (42.9) 4 ( 57.1) \n", | |
| " 2 2 (28.6) 3 ( 42.9) \n", | |
| " 3 0 ( 0.0) 0 ( 0.0) \n", | |
| " 4 2 (28.6) 0 ( 0.0) \n", | |
| " 6 0 ( 0.0) 0 ( 0.0) \n", | |
| " 8 0 ( 0.0) 0 ( 0.0) \n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "# store the object in a variable (t1)\n", | |
| "t1 <- CreateTableOne(data = mtcars, vars = vars, strata = strata,\n", | |
| " factorVars = cat_vars, test = FALSE)\n", | |
| "\n", | |
| "# adjust print options\n", | |
| "print(t1, nonnormal = c(\"hp\", \"wt\"), test = FALSE)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "A more comprehensive resource can be found [here](https://cran.r-project.org/web/packages/tableone/vignettes/introduction.html)." | |
| ] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "R", | |
| "language": "R", | |
| "name": "conda-env-r-r" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": "r", | |
| "file_extension": ".r", | |
| "mimetype": "text/x-r-source", | |
| "name": "R", | |
| "pygments_lexer": "r", | |
| "version": "3.5.1" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 4 | |
| } |
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