Exploration of Flu Data

LOADING REQUIRED PACKAGES

library(here)

here() starts at /Users/shiwanisapkota/Desktop/MADA Course/shiwanisapkota-MADA-portfolio

library(tidyverse)

── Attaching packages
───────────────────────────────────────
tidyverse 1.3.2 ──

✔ ggplot2 3.4.0     ✔ purrr   0.3.4
✔ tibble  3.1.8     ✔ dplyr   1.1.0
✔ tidyr   1.2.0     ✔ stringr 1.4.1
✔ readr   2.1.2     ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(dplyr)
library(ggplot2)

LOADING DATA

fludata_clean <- readRDS(here("fluanalysis", "data", "fludata_clean.rds"))
glimpse(fludata_clean)

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, …

DATA EXPLORATION

Creating summary of data variables

# Creating summary of all variables
summary(fludata_clean)

 SwollenLymphNodes ChestCongestion ChillsSweats NasalCongestion CoughYN  
 No :418           No :323         No :130      No :167         No : 75  
 Yes:312           Yes:407         Yes:600      Yes:563         Yes:655  
                                                                         
                                                                         
                                                                         
                                                                         
 Sneeze    Fatigue   SubjectiveFever Headache      Weakness   WeaknessYN
 No :339   No : 64   No :230         No :115   None    : 49   No : 49   
 Yes:391   Yes:666   Yes:500         Yes:615   Mild    :223   Yes:681   
                                               Moderate:338             
                                               Severe  :120             
                                                                        
                                                                        
  CoughIntensity CoughYN2      Myalgia    MyalgiaYN RunnyNose AbPain   
 None    : 47    No : 47   None    : 79   No : 79   No :211   No :639  
 Mild    :154    Yes:683   Mild    :213   Yes:651   Yes:519   Yes: 91  
 Moderate:357              Moderate:325                                
 Severe  :172              Severe  :113                                
                                                                       
                                                                       
 ChestPain Diarrhea  EyePn     Insomnia  ItchyEye  Nausea    EarPn    
 No :497   No :631   No :617   No :315   No :551   No :475   No :568  
 Yes:233   Yes: 99   Yes:113   Yes:415   Yes:179   Yes:255   Yes:162  
                                                                      
                                                                      
                                                                      
                                                                      
 Hearing   Pharyngitis Breathless ToothPn   Vision    Vomit     Wheeze   
 No :700   No :119     No :436    No :565   No :711   No :652   No :510  
 Yes: 30   Yes:611     Yes:294    Yes:165   Yes: 19   Yes: 78   Yes:220  
                                                                         
                                                                         
                                                                         
                                                                         
    BodyTemp     
 Min.   : 97.20  
 1st Qu.: 98.20  
 Median : 98.50  
 Mean   : 98.94  
 3rd Qu.: 99.30  
 Max.   :103.10  

Creating histograms using our outcomes of interest: Body temperature and Nausea

# Creating histogram of Body temperature variable
ggplot(fludata_clean, aes(x = BodyTemp)) +
  geom_histogram()

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

# Creating histogram of Nausea variable
ggplot(fludata_clean, aes(x = Nausea)) +
  geom_histogram(stat = "count")

Warning in geom_histogram(stat = "count"): Ignoring unknown parameters:
`binwidth`, `bins`, and `pad`

# Creating histogram of Nausea and Insomnia variables
ggplot(fludata_clean, aes(x= Nausea, fill = Insomnia)) +
  geom_histogram(stat="count")

Warning in geom_histogram(stat = "count"): Ignoring unknown parameters:
`binwidth`, `bins`, and `pad`

# Creating histogram of Nausea and Breathless variables
ggplot(fludata_clean, aes(x= Nausea, fill = Breathless)) +
  geom_histogram(stat="count")

Warning in geom_histogram(stat = "count"): Ignoring unknown parameters:
`binwidth`, `bins`, and `pad`

Creating boxplots using our outcome of interest: Body temperature

# Creating boxplot of Cough intensity and Body temperature variables
ggplot(fludata_clean, aes(x = factor(CoughIntensity), y = BodyTemp)) +
  geom_boxplot() +
  labs(x = "Cough Intensity", y = "Body Temperature")

# Creating boxplot of Myalgia and Body temperature variables
ggplot(fludata_clean, aes(x = factor(Myalgia), y = BodyTemp)) +
  geom_boxplot() +
  labs(x = "Myalgia", y = "Body Temperature")