library(here)
library(tidyverse)Wrangling
Load packages
Load the data
flu <- readRDS(here("fluanalysis/data/raw_data/SympAct_Any_Pos.Rda"))Let’s take a look at the dataset using glimpse
glimpse(flu)Rows: 735
Columns: 63
$ DxName1 <fct> "Influenza like illness - Clinical Dx", "Acute tonsi…
$ DxName2 <fct> NA, "Influenza like illness - Clinical Dx", "Acute p…
$ DxName3 <fct> NA, NA, NA, NA, NA, NA, NA, NA, "Fever, unspecified"…
$ DxName4 <fct> NA, NA, NA, NA, NA, NA, NA, NA, "Other fatigue", NA,…
$ DxName5 <fct> NA, NA, NA, NA, NA, NA, NA, NA, "Headache", NA, NA, …
$ Unique.Visit <chr> "340_17632125", "340_17794836", "342_17737773", "342…
$ ActivityLevel <int> 10, 6, 2, 2, 5, 3, 4, 0, 0, 5, 9, 1, 3, 6, 5, 2, 2, …
$ ActivityLevelF <fct> 10, 6, 2, 2, 5, 3, 4, 0, 0, 5, 9, 1, 3, 6, 5, 2, 2, …
$ SwollenLymphNodes <fct> Yes, Yes, Yes, Yes, Yes, No, No, No, Yes, No, Yes, Y…
$ ChestCongestion <fct> No, Yes, Yes, Yes, No, No, No, Yes, Yes, Yes, Yes, Y…
$ ChillsSweats <fct> No, No, Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, Yes, …
$ NasalCongestion <fct> No, Yes, Yes, Yes, No, No, No, Yes, Yes, Yes, Yes, Y…
$ CoughYN <fct> Yes, Yes, No, Yes, No, Yes, Yes, Yes, Yes, Yes, No, …
$ Sneeze <fct> No, No, Yes, Yes, No, Yes, No, Yes, No, No, No, No, …
$ Fatigue <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ SubjectiveFever <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, Yes…
$ Headache <fct> Yes, Yes, Yes, Yes, Yes, Yes, No, Yes, Yes, Yes, Yes…
$ Weakness <fct> Mild, Severe, Severe, Severe, Moderate, Moderate, Mi…
$ WeaknessYN <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ CoughIntensity <fct> Severe, Severe, Mild, Moderate, None, Moderate, Seve…
$ CoughYN2 <fct> Yes, Yes, Yes, Yes, No, Yes, Yes, Yes, Yes, Yes, Yes…
$ Myalgia <fct> Mild, Severe, Severe, Severe, Mild, Moderate, Mild, …
$ MyalgiaYN <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ RunnyNose <fct> No, No, Yes, Yes, No, No, Yes, Yes, Yes, Yes, No, No…
$ AbPain <fct> No, No, Yes, No, No, No, No, No, No, No, Yes, Yes, N…
$ ChestPain <fct> No, No, Yes, No, No, Yes, Yes, No, No, No, No, Yes, …
$ Diarrhea <fct> No, No, No, No, No, Yes, No, No, No, No, No, No, No,…
$ EyePn <fct> No, No, No, No, Yes, No, No, No, No, No, Yes, No, Ye…
$ Insomnia <fct> No, No, Yes, Yes, Yes, No, No, Yes, Yes, Yes, Yes, Y…
$ ItchyEye <fct> No, No, No, No, No, No, No, No, No, No, No, No, Yes,…
$ Nausea <fct> No, No, Yes, Yes, Yes, Yes, No, No, Yes, Yes, Yes, Y…
$ EarPn <fct> No, Yes, No, Yes, No, No, No, No, No, No, No, Yes, Y…
$ Hearing <fct> No, Yes, No, No, No, No, No, No, No, No, No, No, No,…
$ Pharyngitis <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, No, No, Yes, …
$ Breathless <fct> No, No, Yes, No, No, Yes, No, No, No, Yes, No, Yes, …
$ ToothPn <fct> No, No, Yes, No, No, No, No, No, Yes, No, No, Yes, N…
$ Vision <fct> No, No, No, No, No, No, No, No, No, No, No, No, No, …
$ Vomit <fct> No, No, No, No, No, No, Yes, No, No, No, Yes, Yes, N…
$ Wheeze <fct> No, No, No, Yes, No, Yes, No, No, No, No, No, Yes, N…
$ BodyTemp <dbl> 98.3, 100.4, 100.8, 98.8, 100.5, 98.4, 102.5, 98.4, …
$ RapidFluA <fct> Presumptive Negative For Influenza A, NA, Presumptiv…
$ RapidFluB <fct> Presumptive Negative For Influenza B, NA, Presumptiv…
$ PCRFluA <fct> NA, NA, NA, NA, NA, NA, Influenza A Not Detected, N…
$ PCRFluB <fct> NA, NA, NA, NA, NA, NA, Influenza B Not Detected, N…
$ TransScore1 <dbl> 1, 3, 4, 5, 0, 2, 2, 5, 4, 4, 2, 3, 2, 5, 3, 5, 1, 5…
$ TransScore1F <fct> 1, 3, 4, 5, 0, 2, 2, 5, 4, 4, 2, 3, 2, 5, 3, 5, 1, 5…
$ TransScore2 <dbl> 1, 2, 3, 4, 0, 2, 2, 4, 3, 3, 1, 2, 2, 4, 2, 4, 1, 4…
$ TransScore2F <fct> 1, 2, 3, 4, 0, 2, 2, 4, 3, 3, 1, 2, 2, 4, 2, 4, 1, 4…
$ TransScore3 <dbl> 1, 1, 2, 3, 0, 2, 2, 3, 2, 2, 0, 1, 1, 3, 1, 3, 1, 3…
$ TransScore3F <fct> 1, 1, 2, 3, 0, 2, 2, 3, 2, 2, 0, 1, 1, 3, 1, 3, 1, 3…
$ TransScore4 <dbl> 0, 2, 4, 4, 0, 1, 1, 4, 3, 3, 2, 2, 2, 4, 3, 4, 0, 4…
$ TransScore4F <fct> 0, 2, 4, 4, 0, 1, 1, 4, 3, 3, 2, 2, 2, 4, 3, 4, 0, 4…
$ ImpactScore <int> 7, 8, 14, 12, 11, 12, 8, 7, 10, 7, 13, 17, 11, 13, 9…
$ ImpactScore2 <int> 6, 7, 13, 11, 10, 11, 7, 6, 9, 6, 12, 16, 10, 12, 8,…
$ ImpactScore3 <int> 3, 4, 9, 7, 6, 7, 3, 3, 6, 4, 7, 11, 6, 8, 4, 4, 5, …
$ ImpactScoreF <fct> 7, 8, 14, 12, 11, 12, 8, 7, 10, 7, 13, 17, 11, 13, 9…
$ ImpactScore2F <fct> 6, 7, 13, 11, 10, 11, 7, 6, 9, 6, 12, 16, 10, 12, 8,…
$ ImpactScore3F <fct> 3, 4, 9, 7, 6, 7, 3, 3, 6, 4, 7, 11, 6, 8, 4, 4, 5, …
$ ImpactScoreFD <fct> 7, 8, 14, 12, 11, 12, 8, 7, 10, 7, 13, 17, 11, 13, 9…
$ TotalSymp1 <dbl> 8, 11, 18, 17, 11, 14, 10, 12, 14, 11, 15, 20, 13, 1…
$ TotalSymp1F <fct> 8, 11, 18, 17, 11, 14, 10, 12, 14, 11, 15, 20, 13, 1…
$ TotalSymp2 <dbl> 8, 10, 17, 16, 11, 14, 10, 11, 13, 10, 14, 19, 13, 1…
$ TotalSymp3 <dbl> 8, 9, 16, 15, 11, 14, 10, 10, 12, 9, 13, 18, 12, 16,…Now that we have an idea of what the data looks like, let’s drop variables we won’t be using in our analysis using select and remove missing observations.
flu <- flu %>%
select(-contains(c("Score", "Flu")),
-starts_with(c("DxName", "Activity", "Total", "Unique.Visit"))) %>%
drop_na()
glimpse(flu)Rows: 730
Columns: 32
$ SwollenLymphNodes <fct> Yes, Yes, Yes, Yes, Yes, No, No, No, Yes, No, Yes, Y…
$ ChestCongestion <fct> No, Yes, Yes, Yes, No, No, No, Yes, Yes, Yes, Yes, Y…
$ ChillsSweats <fct> No, No, Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, Yes, …
$ NasalCongestion <fct> No, Yes, Yes, Yes, No, No, No, Yes, Yes, Yes, Yes, Y…
$ CoughYN <fct> Yes, Yes, No, Yes, No, Yes, Yes, Yes, Yes, Yes, No, …
$ Sneeze <fct> No, No, Yes, Yes, No, Yes, No, Yes, No, No, No, No, …
$ Fatigue <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ SubjectiveFever <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, Yes…
$ Headache <fct> Yes, Yes, Yes, Yes, Yes, Yes, No, Yes, Yes, Yes, Yes…
$ Weakness <fct> Mild, Severe, Severe, Severe, Moderate, Moderate, Mi…
$ WeaknessYN <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ CoughIntensity <fct> Severe, Severe, Mild, Moderate, None, Moderate, Seve…
$ CoughYN2 <fct> Yes, Yes, Yes, Yes, No, Yes, Yes, Yes, Yes, Yes, Yes…
$ Myalgia <fct> Mild, Severe, Severe, Severe, Mild, Moderate, Mild, …
$ MyalgiaYN <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Yes, Ye…
$ RunnyNose <fct> No, No, Yes, Yes, No, No, Yes, Yes, Yes, Yes, No, No…
$ AbPain <fct> No, No, Yes, No, No, No, No, No, No, No, Yes, Yes, N…
$ ChestPain <fct> No, No, Yes, No, No, Yes, Yes, No, No, No, No, Yes, …
$ Diarrhea <fct> No, No, No, No, No, Yes, No, No, No, No, No, No, No,…
$ EyePn <fct> No, No, No, No, Yes, No, No, No, No, No, Yes, No, Ye…
$ Insomnia <fct> No, No, Yes, Yes, Yes, No, No, Yes, Yes, Yes, Yes, Y…
$ ItchyEye <fct> No, No, No, No, No, No, No, No, No, No, No, No, Yes,…
$ Nausea <fct> No, No, Yes, Yes, Yes, Yes, No, No, Yes, Yes, Yes, Y…
$ EarPn <fct> No, Yes, No, Yes, No, No, No, No, No, No, No, Yes, Y…
$ Hearing <fct> No, Yes, No, No, No, No, No, No, No, No, No, No, No,…
$ Pharyngitis <fct> Yes, Yes, Yes, Yes, Yes, Yes, Yes, No, No, No, Yes, …
$ Breathless <fct> No, No, Yes, No, No, Yes, No, No, No, Yes, No, Yes, …
$ ToothPn <fct> No, No, Yes, No, No, No, No, No, Yes, No, No, Yes, N…
$ Vision <fct> No, No, No, No, No, No, No, No, No, No, No, No, No, …
$ Vomit <fct> No, No, No, No, No, No, Yes, No, No, No, Yes, Yes, N…
$ Wheeze <fct> No, No, No, Yes, No, Yes, No, No, No, No, No, Yes, N…
$ BodyTemp <dbl> 98.3, 100.4, 100.8, 98.8, 100.5, 98.4, 102.5, 98.4, …saveRDS(flu, here("fluanalysis/data/processed_data/flu.rds"))