Exploration

library(here)
library(tidyverse)

flu <- readRDS(here("fluanalysis/data/processed_data/flu.rds"))

Let’s take a look at some summary statistics for BodyTemp and Nausea

summary(flu$BodyTemp)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  97.20   98.20   98.50   98.94   99.30  103.10 

summary(flu$Nausea)

 No Yes 
475 255 

Next, let’s take a look at this distribution of BodyTemp.

flu  %>% ggplot(aes(x = BodyTemp))  + geom_histogram(bins = 20)

I’m also interested in the intensity variables… Let’s make a box plot of a couple of these with BodyTemp.

flu %>% ggplot(aes(x= BodyTemp, y = Myalgia, color = Myalgia)) +
  geom_boxplot() 

flu %>% ggplot(aes(x= BodyTemp, y = Weakness, color = Weakness)) +
  geom_boxplot()

Median body temperature appears to increase with increasing intensity of myalgia/ weakness.

Let’s look at this as a histogram for weakness.

flu  %>% ggplot(aes(x = BodyTemp, fill = Weakness)) + 
  geom_histogram(bins = 20) 

Weakness by Nausea contingency table

table(flu$Weakness,flu$Nausea)

          
            No Yes
  None      39  10
  Mild     172  51
  Moderate 210 128
  Severe    54  66

Myalgia by Nausea contingency table

table(flu$Myalgia,flu$Nausea)

          
            No Yes
  None      63  16
  Mild     159  54
  Moderate 198 127
  Severe    55  58

Cough Intensity by Nausea contingency table

table(flu$CoughIntensity,flu$Nausea)

          
            No Yes
  None      30  17
  Mild      99  55
  Moderate 232 125
  Severe   114  58

Now let’s take visualize this.

flu %>% ggplot(aes(x= Weakness, fill = CoughIntensity)) +
  geom_histogram(stat="count")

flu %>% ggplot(aes(x= Weakness, fill = Myalgia)) +
  geom_histogram(stat="count")

flu %>% ggplot(aes(x= Weakness, fill = Nausea)) +
  geom_histogram(stat="count")

Weakness by Nausea contingency table

table(flu$Weakness,flu$Myalgia)

          
           None Mild Moderate Severe
  None       22   22        5      0
  Mild       37  120       62      4
  Moderate   18   64      208     48
  Severe      2    7       50     61