Flu Analysis Wrangling

Load 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()

library(here)

here() starts at C:/Users/annab/Documents/MADA/annabellahines-MADA-portfolio

Load Raw Data

flu<- readRDS("../data/SympAct_Any_Pos.Rda")

Clean Data

#selecting for variables that don't contain the following character strings of Score, Total, FluA, FluB, Dxname, Activity, or Unique.Visit.
flurevised <- flu %>% select(-matches("Score|Total|FluA|FluB|Dxname|Activity|Unique.visit"))
#remove NAs
flurev <- flurevised %>% drop_na()
#confirm correct number of variables(32) and observations(730)
glimpse(flurev)

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, …

Save Cleaned Data

#save to RDS file
saveRDS(flurev, file="../data/flurevised.rds")