#load in necessary packages
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0 ✔ purrr 1.0.1
✔ tibble 3.1.8 ✔ dplyr 1.0.10
✔ tidyr 1.2.1 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()#load in the cleaned data
flurevise<- readRDS(file = "../data/flurevised.rds")
glimpse(flurevise)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, …#get a summary of the variables
flurevise %>% select(BodyTemp, Nausea) %>% summary() BodyTemp Nausea
Min. : 97.20 No :475
1st Qu.: 98.20 Yes:255
Median : 98.50
Mean : 98.94
3rd Qu.: 99.30
Max. :103.10 #create a histogram of the continuous variable BodyTemp
ggplot(flurevise, aes(x=BodyTemp))+geom_histogram()+labs(title="Body Temperature Frequencies", x="Body Temperature", y="Count")+theme_bw()`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
The distribution looks fairly normal with most of the temps at normal human ranges from around 98-99 degrees, with nothing looking implausible. There are a few across the 100-103 range which could be considered indicative of a fever.
ggplot(flurevise, aes(x=Nausea, y=BodyTemp, fill=Nausea))+geom_boxplot()
Here I was checking how the two outcomes of interest compared to each other in a box plot, they have a pretty even body temperature distribution between those that reported nausea and those that didn’t.
ggplot(flurevise, aes(x=SwollenLymphNodes, y=BodyTemp, fill=SwollenLymphNodes))+geom_boxplot()+labs(title = "Body Temperature Distribution by Lymph Node Status", x="Swollen Lymph Nodes", y="Body Temperature")
It seems from a glance that body temperatures were slightly higher in people who reported no swollen lymph nodes.
ggplot(flurevise, aes(x=CoughIntensity, y=BodyTemp, fill=CoughIntensity))+geom_boxplot()+labs(x="Cough Intensity", y="Body Temperature", title="Body Temperature Distribution by Cough Intensity")
Body temperature tended to trend higher with more intense coughing.
ggplot(flurevise, aes(x=RunnyNose, y=BodyTemp, fill=RunnyNose))+geom_boxplot()+labs(title="Body Temperature Distribution by Presence of Runny Nose", x="Runny Nose Status", y="Body Temperature")