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August 18, 2020 07:35
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "# Merging/Joining data.frames in base R and with dplyr" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "First off we will build a dataset to work with. The data consists of several imaginary medical data forms. A baseline form, a pyschologocal form, a sports form and a medication form. the first three (baseline, psych, sport) forms contain only unique IDs. The forth form can include IDs more than once. If you are not interested in the data generation process you can skip forward to **\"This is where we start to perform merging/joining\"**." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "library(dplyr)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<style>\n", | |
| ".list-inline {list-style: none; margin:0; padding: 0}\n", | |
| ".list-inline>li {display: inline-block}\n", | |
| ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n", | |
| "</style>\n", | |
| "<ol class=list-inline><li>'Pat-5611'</li><li>'Pat-5517'</li><li>'Pat-1591'</li><li>'Pat-4630'</li><li>'Pat-3985'</li><li>'Pat-3649'</li></ol>\n" | |
| ], | |
| "text/latex": [ | |
| "\\begin{enumerate*}\n", | |
| "\\item 'Pat-5611'\n", | |
| "\\item 'Pat-5517'\n", | |
| "\\item 'Pat-1591'\n", | |
| "\\item 'Pat-4630'\n", | |
| "\\item 'Pat-3985'\n", | |
| "\\item 'Pat-3649'\n", | |
| "\\end{enumerate*}\n" | |
| ], | |
| "text/markdown": [ | |
| "1. 'Pat-5611'\n", | |
| "2. 'Pat-5517'\n", | |
| "3. 'Pat-1591'\n", | |
| "4. 'Pat-4630'\n", | |
| "5. 'Pat-3985'\n", | |
| "6. 'Pat-3649'\n", | |
| "\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| "[1] \"Pat-5611\" \"Pat-5517\" \"Pat-1591\" \"Pat-4630\" \"Pat-3985\" \"Pat-3649\"" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# reproducibly create 1000 patient IDs\n", | |
| "set.seed(1337)\n", | |
| "id_num <- sample(x = 1000:9000, size = 1000, replace = FALSE)\n", | |
| "id <- paste0(\"Pat-\", id_num)\n", | |
| "head(id)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 5</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id</th><th scope=col>gender</th><th scope=col>age</th><th scope=col>weight</th><th scope=col>height</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><int></th><th scope=col><int></th><th scope=col><int></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-5611</td><td>female</td><td>72</td><td>54</td><td>153</td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-5517</td><td>female</td><td>78</td><td>60</td><td>156</td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-1591</td><td>male </td><td>75</td><td>74</td><td>159</td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-4630</td><td>male </td><td>18</td><td>87</td><td>189</td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-3985</td><td>male </td><td>48</td><td>55</td><td>165</td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-3649</td><td>male </td><td>74</td><td>79</td><td>153</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 5\n", | |
| "\\begin{tabular}{r|lllll}\n", | |
| " & id & gender & age & weight & height\\\\\n", | |
| " & <fct> & <fct> & <int> & <int> & <int>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-5611 & female & 72 & 54 & 153\\\\\n", | |
| "\t2 & Pat-5517 & female & 78 & 60 & 156\\\\\n", | |
| "\t3 & Pat-1591 & male & 75 & 74 & 159\\\\\n", | |
| "\t4 & Pat-4630 & male & 18 & 87 & 189\\\\\n", | |
| "\t5 & Pat-3985 & male & 48 & 55 & 165\\\\\n", | |
| "\t6 & Pat-3649 & male & 74 & 79 & 153\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 5\n", | |
| "\n", | |
| "| <!--/--> | id <fct> | gender <fct> | age <int> | weight <int> | height <int> |\n", | |
| "|---|---|---|---|---|---|\n", | |
| "| 1 | Pat-5611 | female | 72 | 54 | 153 |\n", | |
| "| 2 | Pat-5517 | female | 78 | 60 | 156 |\n", | |
| "| 3 | Pat-1591 | male | 75 | 74 | 159 |\n", | |
| "| 4 | Pat-4630 | male | 18 | 87 | 189 |\n", | |
| "| 5 | Pat-3985 | male | 48 | 55 | 165 |\n", | |
| "| 6 | Pat-3649 | male | 74 | 79 | 153 |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id gender age weight height\n", | |
| "1 Pat-5611 female 72 54 153 \n", | |
| "2 Pat-5517 female 78 60 156 \n", | |
| "3 Pat-1591 male 75 74 159 \n", | |
| "4 Pat-4630 male 18 87 189 \n", | |
| "5 Pat-3985 male 48 55 165 \n", | |
| "6 Pat-3649 male 74 79 153 " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# create baseline form\n", | |
| "gender <- sample(c(\"male\", \"female\"), size = 1000, replace = TRUE)\n", | |
| "age <- sample(18:99, size = 1000, replace = TRUE)\n", | |
| "weight <- sample(50:100, size = 1000, replace = TRUE)\n", | |
| "height <- sample(140:220, size = 1000, replace = TRUE)\n", | |
| "\n", | |
| "form_bl <- data.frame(id, gender, age, weight, height)\n", | |
| "head(form_bl)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 4</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id_psych</th><th scope=col>happy</th><th scope=col>therapist</th><th scope=col>partner</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-3279</td><td>yes</td><td>yes</td><td>yes</td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-7052</td><td>yes</td><td>yes</td><td>no </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-1492</td><td>no </td><td>no </td><td>yes</td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-3363</td><td>no </td><td>no </td><td>no </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-2073</td><td>no </td><td>no </td><td>yes</td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-2835</td><td>no </td><td>no </td><td>no </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 4\n", | |
| "\\begin{tabular}{r|llll}\n", | |
| " & id\\_psych & happy & therapist & partner\\\\\n", | |
| " & <fct> & <fct> & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-3279 & yes & yes & yes\\\\\n", | |
| "\t2 & Pat-7052 & yes & yes & no \\\\\n", | |
| "\t3 & Pat-1492 & no & no & yes\\\\\n", | |
| "\t4 & Pat-3363 & no & no & no \\\\\n", | |
| "\t5 & Pat-2073 & no & no & yes\\\\\n", | |
| "\t6 & Pat-2835 & no & no & no \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 4\n", | |
| "\n", | |
| "| <!--/--> | id_psych <fct> | happy <fct> | therapist <fct> | partner <fct> |\n", | |
| "|---|---|---|---|---|\n", | |
| "| 1 | Pat-3279 | yes | yes | yes |\n", | |
| "| 2 | Pat-7052 | yes | yes | no |\n", | |
| "| 3 | Pat-1492 | no | no | yes |\n", | |
| "| 4 | Pat-3363 | no | no | no |\n", | |
| "| 5 | Pat-2073 | no | no | yes |\n", | |
| "| 6 | Pat-2835 | no | no | no |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id_psych happy therapist partner\n", | |
| "1 Pat-3279 yes yes yes \n", | |
| "2 Pat-7052 yes yes no \n", | |
| "3 Pat-1492 no no yes \n", | |
| "4 Pat-3363 no no no \n", | |
| "5 Pat-2073 no no yes \n", | |
| "6 Pat-2835 no no no " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# create psych questionnaire form for 100 patients\n", | |
| "id_psych <- sample(id, size = 100, replace = FALSE)\n", | |
| "happy <- sample(c(\"yes\", \"no\"), size = 100, replace = TRUE)\n", | |
| "therapist <- sample(c(\"yes\", \"no\"), size = 100, replace = TRUE)\n", | |
| "partner <- sample(c(\"yes\", \"no\"), size = 100, replace = TRUE)\n", | |
| "\n", | |
| "form_psych <- data.frame(id_psych, happy, therapist, partner)\n", | |
| "head(form_psych)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 3</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id_sport</th><th scope=col>sport_type</th><th scope=col>days_per_week</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><int></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-1216</td><td>Run </td><td>3</td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-1550</td><td>Bike</td><td>2</td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-2299</td><td>Bike</td><td>5</td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-6787</td><td>Bike</td><td>4</td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-7973</td><td>Swim</td><td>2</td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-2729</td><td>Bike</td><td>7</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 3\n", | |
| "\\begin{tabular}{r|lll}\n", | |
| " & id\\_sport & sport\\_type & days\\_per\\_week\\\\\n", | |
| " & <fct> & <fct> & <int>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-1216 & Run & 3\\\\\n", | |
| "\t2 & Pat-1550 & Bike & 2\\\\\n", | |
| "\t3 & Pat-2299 & Bike & 5\\\\\n", | |
| "\t4 & Pat-6787 & Bike & 4\\\\\n", | |
| "\t5 & Pat-7973 & Swim & 2\\\\\n", | |
| "\t6 & Pat-2729 & Bike & 7\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 3\n", | |
| "\n", | |
| "| <!--/--> | id_sport <fct> | sport_type <fct> | days_per_week <int> |\n", | |
| "|---|---|---|---|\n", | |
| "| 1 | Pat-1216 | Run | 3 |\n", | |
| "| 2 | Pat-1550 | Bike | 2 |\n", | |
| "| 3 | Pat-2299 | Bike | 5 |\n", | |
| "| 4 | Pat-6787 | Bike | 4 |\n", | |
| "| 5 | Pat-7973 | Swim | 2 |\n", | |
| "| 6 | Pat-2729 | Bike | 7 |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id_sport sport_type days_per_week\n", | |
| "1 Pat-1216 Run 3 \n", | |
| "2 Pat-1550 Bike 2 \n", | |
| "3 Pat-2299 Bike 5 \n", | |
| "4 Pat-6787 Bike 4 \n", | |
| "5 Pat-7973 Swim 2 \n", | |
| "6 Pat-2729 Bike 7 " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# create sports questionnaire from for 200 patients\n", | |
| "id_sport <- sample(id, size = 200, replace = FALSE)\n", | |
| "sport_type <- sample(c(\"Run\", \"Swim\", \"Bike\"), size = 200, replace = TRUE)\n", | |
| "days_per_week <- sample(1:7, size = 200, replace = TRUE)\n", | |
| "\n", | |
| "form_sport <- data.frame(id_sport, sport_type, days_per_week)\n", | |
| "head(form_sport)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 2</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id_meds</th><th scope=col>med_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-5105</td><td>Lisinopril </td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-5105</td><td>Lipitor </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-5105</td><td>Azithromycin </td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-5105</td><td>Metformin </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-8181</td><td>Lipitor </td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-8181</td><td>Levothyroxine</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 2\n", | |
| "\\begin{tabular}{r|ll}\n", | |
| " & id\\_meds & med\\_type\\\\\n", | |
| " & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-5105 & Lisinopril \\\\\n", | |
| "\t2 & Pat-5105 & Lipitor \\\\\n", | |
| "\t3 & Pat-5105 & Azithromycin \\\\\n", | |
| "\t4 & Pat-5105 & Metformin \\\\\n", | |
| "\t5 & Pat-8181 & Lipitor \\\\\n", | |
| "\t6 & Pat-8181 & Levothyroxine\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 2\n", | |
| "\n", | |
| "| <!--/--> | id_meds <fct> | med_type <fct> |\n", | |
| "|---|---|---|\n", | |
| "| 1 | Pat-5105 | Lisinopril |\n", | |
| "| 2 | Pat-5105 | Lipitor |\n", | |
| "| 3 | Pat-5105 | Azithromycin |\n", | |
| "| 4 | Pat-5105 | Metformin |\n", | |
| "| 5 | Pat-8181 | Lipitor |\n", | |
| "| 6 | Pat-8181 | Levothyroxine |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id_meds med_type \n", | |
| "1 Pat-5105 Lisinopril \n", | |
| "2 Pat-5105 Lipitor \n", | |
| "3 Pat-5105 Azithromycin \n", | |
| "4 Pat-5105 Metformin \n", | |
| "5 Pat-8181 Lipitor \n", | |
| "6 Pat-8181 Levothyroxine" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# create medication and morbidity form for 20 patients with one line per medication/morbidity\n", | |
| "# meds\n", | |
| "id_meds <- sample(id, size = 20, replace = FALSE)\n", | |
| "med_types <- c(\"Lisinopril\", \"Levothyroxine\", \"Azithromycin\",\n", | |
| " \"Metformin\", \"Lipitor\", \"Hydrochlorothiazide\")\n", | |
| "form_meds <- as.data.frame(matrix(nrow = 0, ncol = 2))\n", | |
| "for(i in 1:20) {\n", | |
| " n <- sample(1:6, 1)\n", | |
| " curr_id <- rep(id_meds[i], n)\n", | |
| " med_sample <- sample(med_types, size = n, replace = FALSE)\n", | |
| " form_meds <- rbind(form_meds, data.frame(curr_id, med_sample))\n", | |
| "}\n", | |
| "names(form_meds) <- c(\"id_meds\", \"med_type\")\n", | |
| "head(form_meds)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 2</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id_morb</th><th scope=col>morb_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-5105</td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-8181</td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-8181</td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-4919</td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-7693</td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-7693</td><td>Parkinsons</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 2\n", | |
| "\\begin{tabular}{r|ll}\n", | |
| " & id\\_morb & morb\\_type\\\\\n", | |
| " & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-5105 & Cancer \\\\\n", | |
| "\t2 & Pat-8181 & COPD \\\\\n", | |
| "\t3 & Pat-8181 & Parkinsons\\\\\n", | |
| "\t4 & Pat-4919 & Parkinsons\\\\\n", | |
| "\t5 & Pat-7693 & COPD \\\\\n", | |
| "\t6 & Pat-7693 & Parkinsons\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 2\n", | |
| "\n", | |
| "| <!--/--> | id_morb <fct> | morb_type <fct> |\n", | |
| "|---|---|---|\n", | |
| "| 1 | Pat-5105 | Cancer |\n", | |
| "| 2 | Pat-8181 | COPD |\n", | |
| "| 3 | Pat-8181 | Parkinsons |\n", | |
| "| 4 | Pat-4919 | Parkinsons |\n", | |
| "| 5 | Pat-7693 | COPD |\n", | |
| "| 6 | Pat-7693 | Parkinsons |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id_morb morb_type \n", | |
| "1 Pat-5105 Cancer \n", | |
| "2 Pat-8181 COPD \n", | |
| "3 Pat-8181 Parkinsons\n", | |
| "4 Pat-4919 Parkinsons\n", | |
| "5 Pat-7693 COPD \n", | |
| "6 Pat-7693 Parkinsons" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# morbidity\n", | |
| "morb_types <- c(\"Cancer\", \"HIV\", \"COPD\", \"Parkinsons\")\n", | |
| "form_morb <- as.data.frame(matrix(nrow = 0, ncol = 2))\n", | |
| "for(i in 1:20) {\n", | |
| " n <- sample(1:4, 1)\n", | |
| " curr_id <- rep(id_meds[i], n)\n", | |
| " morb_sample <- sample(morb_types, size = n, replace = FALSE)\n", | |
| " form_morb <- rbind(form_morb, data.frame(curr_id, morb_sample))\n", | |
| "}\n", | |
| "names(form_morb) <- c(\"id_morb\", \"morb_type\")\n", | |
| "head(form_morb)" | |
| ] | |
| }, | |
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| } | |
| ], | |
| "source": [ | |
| "# check ids presence\n", | |
| "all(form_psych$id_psych %in% form_bl$id)\n", | |
| "all(form_sport$id_sport %in% form_bl$id)\n", | |
| "all(form_psych$id_psych %in% form_sport$id_sport)\n", | |
| "all(form_sport$id_sport %in% form_psych$id_psych)\n", | |
| "all(form_meds$id_meds %in% form_bl$id)\n", | |
| "all(form_meds$id_meds %in% form_sport$id_sport)\n", | |
| "all(form_meds$id_meds %in% form_psych$id_psych)\n", | |
| "# how many ids in sport and psych match?\n", | |
| "length(which(form_sport$id_sport %in% form_psych$id_psych))\n", | |
| "# how many ids in sport and meds match?\n", | |
| "length(which(form_sport$id_sport %in% unique(form_meds$id_meds)))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "# This is where we start to perform merging/joining." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 10, | |
| "metadata": {}, | |
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| "<ol class=list-inline><li>200</li><li>7</li></ol>\n" | |
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| "source": [ | |
| "# merging procedures baseR\n", | |
| "bl_sport <- merge(form_bl, form_sport,\n", | |
| " by.x = \"id\", by.y = \"id_sport\")\n", | |
| "bl_sport_all_x <- merge(form_bl, form_sport,\n", | |
| " by.x = \"id\", by.y = \"id_sport\",\n", | |
| " all.x = TRUE)\n", | |
| "psych_sport <- merge(form_psych, form_sport,\n", | |
| " by.x = \"id_psych\", by.y = \"id_sport\")\n", | |
| "psych_sport_all_x <- merge(form_psych, form_sport,\n", | |
| " by.x = \"id_psych\", by.y = \"id_sport\",\n", | |
| " all.x = TRUE)\n", | |
| "psych_sport_all_y <- merge(form_psych, form_sport,\n", | |
| " by.x = \"id_psych\", by.y = \"id_sport\",\n", | |
| " all.y = TRUE)\n", | |
| "psych_sport_all_x_and_y <- merge(form_psych, form_sport,\n", | |
| " by.x = \"id_psych\", by.y = \"id_sport\",\n", | |
| " all.x = TRUE, all.y = TRUE)\n", | |
| "\n", | |
| "dim(bl_sport)\n", | |
| "dim(bl_sport_all_x)\n", | |
| "dim(psych_sport)\n", | |
| "dim(psych_sport_all_x)\n", | |
| "dim(psych_sport_all_y)\n", | |
| "dim(psych_sport_all_x_and_y)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 11, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "Warning message:\n", | |
| "“Column `id`/`id_sport` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id`/`id_sport` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id_psych`/`id_sport` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id_psych`/`id_sport` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id_psych`/`id_sport` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id_psych`/`id_sport` joining factors with different levels, coercing to character vector”" | |
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| "source": [ | |
| "# merging with dplyr joins\n", | |
| "bl_sport_inner <- inner_join(form_bl, form_sport, by = c(\"id\" = \"id_sport\"))\n", | |
| "bl_sport_left <- left_join(form_bl, form_sport, by = c(\"id\" = \"id_sport\"))\n", | |
| "psych_sport_inner <- inner_join(form_psych, form_sport, by = c(\"id_psych\" = \"id_sport\"))\n", | |
| "psych_sport_left <- left_join(form_psych, form_sport, by = c(\"id_psych\" = \"id_sport\"))\n", | |
| "psych_sport_right <- right_join(form_psych, form_sport, by = c(\"id_psych\" = \"id_sport\"))\n", | |
| "psych_sport_full <- full_join(form_psych, form_sport, by = c(\"id_psych\" = \"id_sport\"))\n", | |
| "\n", | |
| "dim(bl_sport_inner)\n", | |
| "dim(bl_sport_left)\n", | |
| "dim(psych_sport_inner)\n", | |
| "dim(psych_sport_left)\n", | |
| "dim(psych_sport_right)\n", | |
| "dim(psych_sport_full)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 12, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "Warning message:\n", | |
| "“Column `id`/`id_meds` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id`/`id_meds` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id`/`id_meds` joining factors with different levels, coercing to character vector”Warning message:\n", | |
| "“Column `id`/`id_meds` joining factors with different levels, coercing to character vector”" | |
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| "source": [ | |
| "# merging with unique and repeated ids\n", | |
| "# baseR\n", | |
| "bl_meds <- merge(x = form_bl, y = form_meds, by.x = \"id\", by.y = \"id_meds\")\n", | |
| "# dplyr\n", | |
| "bl_meds_inner <- inner_join(x = form_bl, y = form_meds, by = c(\"id\" = \"id_meds\"))\n", | |
| "bl_meds_left <- left_join(x = form_bl, y = form_meds, by = c(\"id\" = \"id_meds\"))\n", | |
| "bl_meds_right <- right_join(x = form_bl, y = form_meds, by = c(\"id\" = \"id_meds\"))\n", | |
| "bl_meds_full <- full_join(x = form_bl, y = form_meds, by = c(\"id\" = \"id_meds\"))\n", | |
| "\n", | |
| "nrow(bl_meds_inner)\n", | |
| "nrow(bl_meds_left)\n", | |
| "nrow(bl_meds_right)\n", | |
| "nrow(bl_meds_full)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 13, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 10 × 6</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id</th><th scope=col>gender</th><th scope=col>age</th><th scope=col>weight</th><th scope=col>height</th><th scope=col>med_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><chr></th><th scope=col><fct></th><th scope=col><int></th><th scope=col><int></th><th scope=col><int></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-7578</td><td>male </td><td>98</td><td>65</td><td>187</td><td>Metformin </td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lipitor </td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Metformin </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Hydrochlorothiazide</td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lisinopril </td></tr>\n", | |
| "\t<tr><th scope=row>7</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Azithromycin </td></tr>\n", | |
| "\t<tr><th scope=row>8</th><td>Pat-4964</td><td>male </td><td>66</td><td>73</td><td>196</td><td>Levothyroxine </td></tr>\n", | |
| "\t<tr><th scope=row>9</th><td>Pat-4964</td><td>male </td><td>66</td><td>73</td><td>196</td><td>Metformin </td></tr>\n", | |
| "\t<tr><th scope=row>10</th><td>Pat-4964</td><td>male </td><td>66</td><td>73</td><td>196</td><td>Lipitor </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 10 × 6\n", | |
| "\\begin{tabular}{r|llllll}\n", | |
| " & id & gender & age & weight & height & med\\_type\\\\\n", | |
| " & <chr> & <fct> & <int> & <int> & <int> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-7578 & male & 98 & 65 & 187 & Metformin \\\\\n", | |
| "\t2 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine \\\\\n", | |
| "\t3 & Pat-5350 & female & 20 & 89 & 190 & Lipitor \\\\\n", | |
| "\t4 & Pat-5350 & female & 20 & 89 & 190 & Metformin \\\\\n", | |
| "\t5 & Pat-5350 & female & 20 & 89 & 190 & Hydrochlorothiazide\\\\\n", | |
| "\t6 & Pat-5350 & female & 20 & 89 & 190 & Lisinopril \\\\\n", | |
| "\t7 & Pat-5350 & female & 20 & 89 & 190 & Azithromycin \\\\\n", | |
| "\t8 & Pat-4964 & male & 66 & 73 & 196 & Levothyroxine \\\\\n", | |
| "\t9 & Pat-4964 & male & 66 & 73 & 196 & Metformin \\\\\n", | |
| "\t10 & Pat-4964 & male & 66 & 73 & 196 & Lipitor \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 10 × 6\n", | |
| "\n", | |
| "| <!--/--> | id <chr> | gender <fct> | age <int> | weight <int> | height <int> | med_type <fct> |\n", | |
| "|---|---|---|---|---|---|---|\n", | |
| "| 1 | Pat-7578 | male | 98 | 65 | 187 | Metformin |\n", | |
| "| 2 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine |\n", | |
| "| 3 | Pat-5350 | female | 20 | 89 | 190 | Lipitor |\n", | |
| "| 4 | Pat-5350 | female | 20 | 89 | 190 | Metformin |\n", | |
| "| 5 | Pat-5350 | female | 20 | 89 | 190 | Hydrochlorothiazide |\n", | |
| "| 6 | Pat-5350 | female | 20 | 89 | 190 | Lisinopril |\n", | |
| "| 7 | Pat-5350 | female | 20 | 89 | 190 | Azithromycin |\n", | |
| "| 8 | Pat-4964 | male | 66 | 73 | 196 | Levothyroxine |\n", | |
| "| 9 | Pat-4964 | male | 66 | 73 | 196 | Metformin |\n", | |
| "| 10 | Pat-4964 | male | 66 | 73 | 196 | Lipitor |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id gender age weight height med_type \n", | |
| "1 Pat-7578 male 98 65 187 Metformin \n", | |
| "2 Pat-5350 female 20 89 190 Levothyroxine \n", | |
| "3 Pat-5350 female 20 89 190 Lipitor \n", | |
| "4 Pat-5350 female 20 89 190 Metformin \n", | |
| "5 Pat-5350 female 20 89 190 Hydrochlorothiazide\n", | |
| "6 Pat-5350 female 20 89 190 Lisinopril \n", | |
| "7 Pat-5350 female 20 89 190 Azithromycin \n", | |
| "8 Pat-4964 male 66 73 196 Levothyroxine \n", | |
| "9 Pat-4964 male 66 73 196 Metformin \n", | |
| "10 Pat-4964 male 66 73 196 Lipitor " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "head(bl_meds_inner, n = 10)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 14, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "Warning message:\n", | |
| "“Column `id`/`id_morb` joining character vector and factor, coercing into character vector”" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 7</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id</th><th scope=col>gender</th><th scope=col>age</th><th scope=col>weight</th><th scope=col>height</th><th scope=col>med_type</th><th scope=col>morb_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><chr></th><th scope=col><fct></th><th scope=col><int></th><th scope=col><int></th><th scope=col><int></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>1</th><td>Pat-7578</td><td>male </td><td>98</td><td>65</td><td>187</td><td>Metformin </td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-7578</td><td>male </td><td>98</td><td>65</td><td>187</td><td>Metformin </td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine</td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine</td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine</td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine</td><td>Parkinsons</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 7\n", | |
| "\\begin{tabular}{r|lllllll}\n", | |
| " & id & gender & age & weight & height & med\\_type & morb\\_type\\\\\n", | |
| " & <chr> & <fct> & <int> & <int> & <int> & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t1 & Pat-7578 & male & 98 & 65 & 187 & Metformin & Parkinsons\\\\\n", | |
| "\t2 & Pat-7578 & male & 98 & 65 & 187 & Metformin & COPD \\\\\n", | |
| "\t3 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & COPD \\\\\n", | |
| "\t4 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & HIV \\\\\n", | |
| "\t5 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & Cancer \\\\\n", | |
| "\t6 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & Parkinsons\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 7\n", | |
| "\n", | |
| "| <!--/--> | id <chr> | gender <fct> | age <int> | weight <int> | height <int> | med_type <fct> | morb_type <fct> |\n", | |
| "|---|---|---|---|---|---|---|---|\n", | |
| "| 1 | Pat-7578 | male | 98 | 65 | 187 | Metformin | Parkinsons |\n", | |
| "| 2 | Pat-7578 | male | 98 | 65 | 187 | Metformin | COPD |\n", | |
| "| 3 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | COPD |\n", | |
| "| 4 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | HIV |\n", | |
| "| 5 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | Cancer |\n", | |
| "| 6 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | Parkinsons |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id gender age weight height med_type morb_type \n", | |
| "1 Pat-7578 male 98 65 187 Metformin Parkinsons\n", | |
| "2 Pat-7578 male 98 65 187 Metformin COPD \n", | |
| "3 Pat-5350 female 20 89 190 Levothyroxine COPD \n", | |
| "4 Pat-5350 female 20 89 190 Levothyroxine HIV \n", | |
| "5 Pat-5350 female 20 89 190 Levothyroxine Cancer \n", | |
| "6 Pat-5350 female 20 89 190 Levothyroxine Parkinsons" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# merging repeated and repeated ids\n", | |
| "bl_meds_morb_left <- left_join(bl_meds_inner, form_morb, by = c(\"id\" = \"id_morb\"))\n", | |
| "head(bl_meds_morb_left)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "Below you can see how data is duplicated if you start joining with repeated IDs. Specifically, \"Pat-5350\" starts with one line in the baseline data.frame. When joined with the medication data, the baseline data is repeated six times. Then, when further joining this to the morbidity data, every line is again repeated for each morbidity. At this stage it is clear, that the data.frame no longer is a useful representation of the original data." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 15, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 1 × 5</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id</th><th scope=col>gender</th><th scope=col>age</th><th scope=col>weight</th><th scope=col>height</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th><th scope=col><int></th><th scope=col><int></th><th scope=col><int></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>144</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 1 × 5\n", | |
| "\\begin{tabular}{r|lllll}\n", | |
| " & id & gender & age & weight & height\\\\\n", | |
| " & <fct> & <fct> & <int> & <int> & <int>\\\\\n", | |
| "\\hline\n", | |
| "\t144 & Pat-5350 & female & 20 & 89 & 190\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 1 × 5\n", | |
| "\n", | |
| "| <!--/--> | id <fct> | gender <fct> | age <int> | weight <int> | height <int> |\n", | |
| "|---|---|---|---|---|---|\n", | |
| "| 144 | Pat-5350 | female | 20 | 89 | 190 |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id gender age weight height\n", | |
| "144 Pat-5350 female 20 89 190 " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "form_bl[form_bl$id == \"Pat-5350\", ]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 16, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 2</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id_meds</th><th scope=col>med_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>49</th><td>Pat-5350</td><td>Levothyroxine </td></tr>\n", | |
| "\t<tr><th scope=row>50</th><td>Pat-5350</td><td>Lipitor </td></tr>\n", | |
| "\t<tr><th scope=row>51</th><td>Pat-5350</td><td>Metformin </td></tr>\n", | |
| "\t<tr><th scope=row>52</th><td>Pat-5350</td><td>Hydrochlorothiazide</td></tr>\n", | |
| "\t<tr><th scope=row>53</th><td>Pat-5350</td><td>Lisinopril </td></tr>\n", | |
| "\t<tr><th scope=row>54</th><td>Pat-5350</td><td>Azithromycin </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 2\n", | |
| "\\begin{tabular}{r|ll}\n", | |
| " & id\\_meds & med\\_type\\\\\n", | |
| " & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t49 & Pat-5350 & Levothyroxine \\\\\n", | |
| "\t50 & Pat-5350 & Lipitor \\\\\n", | |
| "\t51 & Pat-5350 & Metformin \\\\\n", | |
| "\t52 & Pat-5350 & Hydrochlorothiazide\\\\\n", | |
| "\t53 & Pat-5350 & Lisinopril \\\\\n", | |
| "\t54 & Pat-5350 & Azithromycin \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 2\n", | |
| "\n", | |
| "| <!--/--> | id_meds <fct> | med_type <fct> |\n", | |
| "|---|---|---|\n", | |
| "| 49 | Pat-5350 | Levothyroxine |\n", | |
| "| 50 | Pat-5350 | Lipitor |\n", | |
| "| 51 | Pat-5350 | Metformin |\n", | |
| "| 52 | Pat-5350 | Hydrochlorothiazide |\n", | |
| "| 53 | Pat-5350 | Lisinopril |\n", | |
| "| 54 | Pat-5350 | Azithromycin |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id_meds med_type \n", | |
| "49 Pat-5350 Levothyroxine \n", | |
| "50 Pat-5350 Lipitor \n", | |
| "51 Pat-5350 Metformin \n", | |
| "52 Pat-5350 Hydrochlorothiazide\n", | |
| "53 Pat-5350 Lisinopril \n", | |
| "54 Pat-5350 Azithromycin " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "form_meds[form_meds$id_meds == \"Pat-5350\", ]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 17, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 4 × 2</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id_morb</th><th scope=col>morb_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>40</th><td>Pat-5350</td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>41</th><td>Pat-5350</td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>42</th><td>Pat-5350</td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>43</th><td>Pat-5350</td><td>Parkinsons</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 4 × 2\n", | |
| "\\begin{tabular}{r|ll}\n", | |
| " & id\\_morb & morb\\_type\\\\\n", | |
| " & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t40 & Pat-5350 & COPD \\\\\n", | |
| "\t41 & Pat-5350 & HIV \\\\\n", | |
| "\t42 & Pat-5350 & Cancer \\\\\n", | |
| "\t43 & Pat-5350 & Parkinsons\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 4 × 2\n", | |
| "\n", | |
| "| <!--/--> | id_morb <fct> | morb_type <fct> |\n", | |
| "|---|---|---|\n", | |
| "| 40 | Pat-5350 | COPD |\n", | |
| "| 41 | Pat-5350 | HIV |\n", | |
| "| 42 | Pat-5350 | Cancer |\n", | |
| "| 43 | Pat-5350 | Parkinsons |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id_morb morb_type \n", | |
| "40 Pat-5350 COPD \n", | |
| "41 Pat-5350 HIV \n", | |
| "42 Pat-5350 Cancer \n", | |
| "43 Pat-5350 Parkinsons" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "form_morb[form_morb$id_morb == \"Pat-5350\", ]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 18, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<caption>A data.frame: 6 × 6</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id</th><th scope=col>gender</th><th scope=col>age</th><th scope=col>weight</th><th scope=col>height</th><th scope=col>med_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><chr></th><th scope=col><fct></th><th scope=col><int></th><th scope=col><int></th><th scope=col><int></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>2</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lipitor </td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Metformin </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Hydrochlorothiazide</td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lisinopril </td></tr>\n", | |
| "\t<tr><th scope=row>7</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Azithromycin </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 6 × 6\n", | |
| "\\begin{tabular}{r|llllll}\n", | |
| " & id & gender & age & weight & height & med\\_type\\\\\n", | |
| " & <chr> & <fct> & <int> & <int> & <int> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t2 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine \\\\\n", | |
| "\t3 & Pat-5350 & female & 20 & 89 & 190 & Lipitor \\\\\n", | |
| "\t4 & Pat-5350 & female & 20 & 89 & 190 & Metformin \\\\\n", | |
| "\t5 & Pat-5350 & female & 20 & 89 & 190 & Hydrochlorothiazide\\\\\n", | |
| "\t6 & Pat-5350 & female & 20 & 89 & 190 & Lisinopril \\\\\n", | |
| "\t7 & Pat-5350 & female & 20 & 89 & 190 & Azithromycin \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 6 × 6\n", | |
| "\n", | |
| "| <!--/--> | id <chr> | gender <fct> | age <int> | weight <int> | height <int> | med_type <fct> |\n", | |
| "|---|---|---|---|---|---|---|\n", | |
| "| 2 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine |\n", | |
| "| 3 | Pat-5350 | female | 20 | 89 | 190 | Lipitor |\n", | |
| "| 4 | Pat-5350 | female | 20 | 89 | 190 | Metformin |\n", | |
| "| 5 | Pat-5350 | female | 20 | 89 | 190 | Hydrochlorothiazide |\n", | |
| "| 6 | Pat-5350 | female | 20 | 89 | 190 | Lisinopril |\n", | |
| "| 7 | Pat-5350 | female | 20 | 89 | 190 | Azithromycin |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id gender age weight height med_type \n", | |
| "2 Pat-5350 female 20 89 190 Levothyroxine \n", | |
| "3 Pat-5350 female 20 89 190 Lipitor \n", | |
| "4 Pat-5350 female 20 89 190 Metformin \n", | |
| "5 Pat-5350 female 20 89 190 Hydrochlorothiazide\n", | |
| "6 Pat-5350 female 20 89 190 Lisinopril \n", | |
| "7 Pat-5350 female 20 89 190 Azithromycin " | |
| ] | |
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| "bl_meds_inner[bl_meds_inner$id == \"Pat-5350\", ]" | |
| ] | |
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| "<table>\n", | |
| "<caption>A data.frame: 24 × 7</caption>\n", | |
| "<thead>\n", | |
| "\t<tr><th></th><th scope=col>id</th><th scope=col>gender</th><th scope=col>age</th><th scope=col>weight</th><th scope=col>height</th><th scope=col>med_type</th><th scope=col>morb_type</th></tr>\n", | |
| "\t<tr><th></th><th scope=col><chr></th><th scope=col><fct></th><th scope=col><int></th><th scope=col><int></th><th scope=col><int></th><th scope=col><fct></th><th scope=col><fct></th></tr>\n", | |
| "</thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>3</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine </td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine </td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine </td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Levothyroxine </td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>7</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lipitor </td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>8</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lipitor </td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>9</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lipitor </td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>10</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lipitor </td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>11</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Metformin </td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>12</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Metformin </td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>13</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Metformin </td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>14</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Metformin </td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>15</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Hydrochlorothiazide</td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>16</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Hydrochlorothiazide</td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>17</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Hydrochlorothiazide</td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>18</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Hydrochlorothiazide</td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>19</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lisinopril </td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>20</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lisinopril </td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>21</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lisinopril </td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>22</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Lisinopril </td><td>Parkinsons</td></tr>\n", | |
| "\t<tr><th scope=row>23</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Azithromycin </td><td>COPD </td></tr>\n", | |
| "\t<tr><th scope=row>24</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Azithromycin </td><td>HIV </td></tr>\n", | |
| "\t<tr><th scope=row>25</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Azithromycin </td><td>Cancer </td></tr>\n", | |
| "\t<tr><th scope=row>26</th><td>Pat-5350</td><td>female</td><td>20</td><td>89</td><td>190</td><td>Azithromycin </td><td>Parkinsons</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "A data.frame: 24 × 7\n", | |
| "\\begin{tabular}{r|lllllll}\n", | |
| " & id & gender & age & weight & height & med\\_type & morb\\_type\\\\\n", | |
| " & <chr> & <fct> & <int> & <int> & <int> & <fct> & <fct>\\\\\n", | |
| "\\hline\n", | |
| "\t3 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & COPD \\\\\n", | |
| "\t4 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & HIV \\\\\n", | |
| "\t5 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & Cancer \\\\\n", | |
| "\t6 & Pat-5350 & female & 20 & 89 & 190 & Levothyroxine & Parkinsons\\\\\n", | |
| "\t7 & Pat-5350 & female & 20 & 89 & 190 & Lipitor & COPD \\\\\n", | |
| "\t8 & Pat-5350 & female & 20 & 89 & 190 & Lipitor & HIV \\\\\n", | |
| "\t9 & Pat-5350 & female & 20 & 89 & 190 & Lipitor & Cancer \\\\\n", | |
| "\t10 & Pat-5350 & female & 20 & 89 & 190 & Lipitor & Parkinsons\\\\\n", | |
| "\t11 & Pat-5350 & female & 20 & 89 & 190 & Metformin & COPD \\\\\n", | |
| "\t12 & Pat-5350 & female & 20 & 89 & 190 & Metformin & HIV \\\\\n", | |
| "\t13 & Pat-5350 & female & 20 & 89 & 190 & Metformin & Cancer \\\\\n", | |
| "\t14 & Pat-5350 & female & 20 & 89 & 190 & Metformin & Parkinsons\\\\\n", | |
| "\t15 & Pat-5350 & female & 20 & 89 & 190 & Hydrochlorothiazide & COPD \\\\\n", | |
| "\t16 & Pat-5350 & female & 20 & 89 & 190 & Hydrochlorothiazide & HIV \\\\\n", | |
| "\t17 & Pat-5350 & female & 20 & 89 & 190 & Hydrochlorothiazide & Cancer \\\\\n", | |
| "\t18 & Pat-5350 & female & 20 & 89 & 190 & Hydrochlorothiazide & Parkinsons\\\\\n", | |
| "\t19 & Pat-5350 & female & 20 & 89 & 190 & Lisinopril & COPD \\\\\n", | |
| "\t20 & Pat-5350 & female & 20 & 89 & 190 & Lisinopril & HIV \\\\\n", | |
| "\t21 & Pat-5350 & female & 20 & 89 & 190 & Lisinopril & Cancer \\\\\n", | |
| "\t22 & Pat-5350 & female & 20 & 89 & 190 & Lisinopril & Parkinsons\\\\\n", | |
| "\t23 & Pat-5350 & female & 20 & 89 & 190 & Azithromycin & COPD \\\\\n", | |
| "\t24 & Pat-5350 & female & 20 & 89 & 190 & Azithromycin & HIV \\\\\n", | |
| "\t25 & Pat-5350 & female & 20 & 89 & 190 & Azithromycin & Cancer \\\\\n", | |
| "\t26 & Pat-5350 & female & 20 & 89 & 190 & Azithromycin & Parkinsons\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "A data.frame: 24 × 7\n", | |
| "\n", | |
| "| <!--/--> | id <chr> | gender <fct> | age <int> | weight <int> | height <int> | med_type <fct> | morb_type <fct> |\n", | |
| "|---|---|---|---|---|---|---|---|\n", | |
| "| 3 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | COPD |\n", | |
| "| 4 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | HIV |\n", | |
| "| 5 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | Cancer |\n", | |
| "| 6 | Pat-5350 | female | 20 | 89 | 190 | Levothyroxine | Parkinsons |\n", | |
| "| 7 | Pat-5350 | female | 20 | 89 | 190 | Lipitor | COPD |\n", | |
| "| 8 | Pat-5350 | female | 20 | 89 | 190 | Lipitor | HIV |\n", | |
| "| 9 | Pat-5350 | female | 20 | 89 | 190 | Lipitor | Cancer |\n", | |
| "| 10 | Pat-5350 | female | 20 | 89 | 190 | Lipitor | Parkinsons |\n", | |
| "| 11 | Pat-5350 | female | 20 | 89 | 190 | Metformin | COPD |\n", | |
| "| 12 | Pat-5350 | female | 20 | 89 | 190 | Metformin | HIV |\n", | |
| "| 13 | Pat-5350 | female | 20 | 89 | 190 | Metformin | Cancer |\n", | |
| "| 14 | Pat-5350 | female | 20 | 89 | 190 | Metformin | Parkinsons |\n", | |
| "| 15 | Pat-5350 | female | 20 | 89 | 190 | Hydrochlorothiazide | COPD |\n", | |
| "| 16 | Pat-5350 | female | 20 | 89 | 190 | Hydrochlorothiazide | HIV |\n", | |
| "| 17 | Pat-5350 | female | 20 | 89 | 190 | Hydrochlorothiazide | Cancer |\n", | |
| "| 18 | Pat-5350 | female | 20 | 89 | 190 | Hydrochlorothiazide | Parkinsons |\n", | |
| "| 19 | Pat-5350 | female | 20 | 89 | 190 | Lisinopril | COPD |\n", | |
| "| 20 | Pat-5350 | female | 20 | 89 | 190 | Lisinopril | HIV |\n", | |
| "| 21 | Pat-5350 | female | 20 | 89 | 190 | Lisinopril | Cancer |\n", | |
| "| 22 | Pat-5350 | female | 20 | 89 | 190 | Lisinopril | Parkinsons |\n", | |
| "| 23 | Pat-5350 | female | 20 | 89 | 190 | Azithromycin | COPD |\n", | |
| "| 24 | Pat-5350 | female | 20 | 89 | 190 | Azithromycin | HIV |\n", | |
| "| 25 | Pat-5350 | female | 20 | 89 | 190 | Azithromycin | Cancer |\n", | |
| "| 26 | Pat-5350 | female | 20 | 89 | 190 | Azithromycin | Parkinsons |\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " id gender age weight height med_type morb_type \n", | |
| "3 Pat-5350 female 20 89 190 Levothyroxine COPD \n", | |
| "4 Pat-5350 female 20 89 190 Levothyroxine HIV \n", | |
| "5 Pat-5350 female 20 89 190 Levothyroxine Cancer \n", | |
| "6 Pat-5350 female 20 89 190 Levothyroxine Parkinsons\n", | |
| "7 Pat-5350 female 20 89 190 Lipitor COPD \n", | |
| "8 Pat-5350 female 20 89 190 Lipitor HIV \n", | |
| "9 Pat-5350 female 20 89 190 Lipitor Cancer \n", | |
| "10 Pat-5350 female 20 89 190 Lipitor Parkinsons\n", | |
| "11 Pat-5350 female 20 89 190 Metformin COPD \n", | |
| "12 Pat-5350 female 20 89 190 Metformin HIV \n", | |
| "13 Pat-5350 female 20 89 190 Metformin Cancer \n", | |
| "14 Pat-5350 female 20 89 190 Metformin Parkinsons\n", | |
| "15 Pat-5350 female 20 89 190 Hydrochlorothiazide COPD \n", | |
| "16 Pat-5350 female 20 89 190 Hydrochlorothiazide HIV \n", | |
| "17 Pat-5350 female 20 89 190 Hydrochlorothiazide Cancer \n", | |
| "18 Pat-5350 female 20 89 190 Hydrochlorothiazide Parkinsons\n", | |
| "19 Pat-5350 female 20 89 190 Lisinopril COPD \n", | |
| "20 Pat-5350 female 20 89 190 Lisinopril HIV \n", | |
| "21 Pat-5350 female 20 89 190 Lisinopril Cancer \n", | |
| "22 Pat-5350 female 20 89 190 Lisinopril Parkinsons\n", | |
| "23 Pat-5350 female 20 89 190 Azithromycin COPD \n", | |
| "24 Pat-5350 female 20 89 190 Azithromycin HIV \n", | |
| "25 Pat-5350 female 20 89 190 Azithromycin Cancer \n", | |
| "26 Pat-5350 female 20 89 190 Azithromycin Parkinsons" | |
| ] | |
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| "metadata": {}, | |
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| } | |
| ], | |
| "source": [ | |
| "bl_meds_morb_left[bl_meds_morb_left$id == \"Pat-5350\", ]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 20, | |
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| "data": { | |
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| "<style>\n", | |
| ".list-inline {list-style: none; margin:0; padding: 0}\n", | |
| ".list-inline>li {display: inline-block}\n", | |
| ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n", | |
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| "<ol class=list-inline><li>'Mersenne-Twister'</li><li>'Inversion'</li></ol>\n" | |
| ], | |
| "text/latex": [ | |
| "\\begin{enumerate*}\n", | |
| "\\item 'Mersenne-Twister'\n", | |
| "\\item 'Inversion'\n", | |
| "\\end{enumerate*}\n" | |
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| "1. 'Mersenne-Twister'\n", | |
| "2. 'Inversion'\n", | |
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| "[1] \"Mersenne-Twister\" \"Inversion\" " | |
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| "source": [ | |
| "RNGkind()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
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| "R version 3.5.1 (2018-07-02)\n", | |
| "Platform: x86_64-conda_cos6-linux-gnu (64-bit)\n", | |
| "Running under: Debian GNU/Linux 10 (buster)\n", | |
| "\n", | |
| "Matrix products: default\n", | |
| "BLAS/LAPACK: /home/jupyterlab/conda/envs/r/lib/R/lib/libRlapack.so\n", | |
| "\n", | |
| "locale:\n", | |
| " [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n", | |
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| "[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n", | |
| "\n", | |
| "attached base packages:\n", | |
| "[1] stats graphics grDevices utils datasets methods base \n", | |
| "\n", | |
| "other attached packages:\n", | |
| "[1] dplyr_0.8.5\n", | |
| "\n", | |
| "loaded via a namespace (and not attached):\n", | |
| " [1] Rcpp_1.0.4.6 assertthat_0.2.1 digest_0.6.25 crayon_1.3.4 \n", | |
| " [5] IRdisplay_0.7.0 repr_1.1.0 R6_2.4.1 lifecycle_0.2.0 \n", | |
| " [9] jsonlite_1.6.1 magrittr_1.5 evaluate_0.14 pillar_1.4.3 \n", | |
| "[13] rlang_0.4.5 uuid_0.1-4 vctrs_0.2.4 ellipsis_0.3.0 \n", | |
| "[17] IRkernel_0.8.12 tools_3.5.1 glue_1.4.0 purrr_0.3.4 \n", | |
| "[21] compiler_3.5.1 pkgconfig_2.0.3 base64enc_0.1-3 htmltools_0.4.0 \n", | |
| "[25] pbdZMQ_0.3-3 tidyselect_1.0.0 tibble_3.0.1 " | |
| ] | |
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| "sessionInfo()" | |
| ] | |
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| "language": "R", | |
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