R/scripts_machine_learning /ML_covid.R

In gabrielburcea/cvindia: Analysis of symptoms

########################################
#### Loading libraries needed #########
#######################################
library(caret)
library(corrplot)
library(tidyverse)
library(e1071)
library(DMwR)
library(lattice)
library(pROC)
library(ROCR)
library(ggplot2)
library(reshape2)
library(leaps)
library(MASS)
library(rms)

######################################
########Reading the data ############
#####################################

data <- read.csv("~/Rprojects/data/PivotMappe060520r.csv", header = TRUE, sep = ",")

######################################################################################################
################ Get the LSHI into different columns as it contains more than 1 string per row #######
######################################################################################################

data_select <- data %>%
  #### rename reason for helping as it contains whether respondents have been tested negative or positive
  dplyr::rename(tested_or_not = 'Reason.For.Helping') %>%
  tidyr::separate('Long.Standing.Health.Issues', c('Comorbidity_one', 'Comorbidity_two', 'Comorbidity_three', 'Comorbidity_four',
                                          'Comorbidity_five', 'Comorbidity_six', 'Comorbidity_seven', 'Comorbidity_eight', 
                                          'Comorbidity_nine'), sep = ",")

data_rec <- data_select  %>%
  tidyr::pivot_longer(cols = starts_with('Comorbidity'), 
                      names_to = 'Comorbidity_count', 
                      values_to = 'Comorbidity') %>%
  tidyr::drop_na('Comorbidity') %>%
  dplyr::select(-Comorbidity_count) %>%
  dplyr::distinct() %>%
  dplyr::mutate(Condition = 2) %>%
  tidyr::pivot_wider(id_cols = -c(Comorbidity, Condition), names_from = Comorbidity, values_from = Condition, values_fill = list(Condition = 1)) %>%
  dplyr::select(-None)

level_key <-
  c(
    None = 'negative',
    Curious = "negative",
    'Showing Symptoms But Not Tested,Curious' = "negative",
    'Showing Symptoms But Not Tested' = "negative",
    'Self-Isolating With No Symptoms' = "negative",
    'Showing Symptoms But Not Tested,Curious,Self-Isolating With No Symptoms' = "negative",
    'Tested Positive' = 'positive',
    'Curious,Self-Isolating With No Symptoms' = 'negative',
    'Tested Negative But Have Symptoms' = 'negative',
    'Recovered But Have New Symptoms' = 'positive',
    'Live With Someone With Coronavirus' = 'positive',
    'Live With Someone With Coronavirus,Curious' = 'negative',
    'Tested Negative But Have Symptoms,Self-Isolating With No Symptoms' = 'negative',
    'Tested Negative But Have Symptoms,Curious' = 'negative',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested' = 'positive',
    'Tested Positive,Self-Isolating With No Symptoms' = 'positive',
    'Showing Symptoms But Not Tested,Self-Isolating With No Symptoms' = 'negative',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'positive',
    'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested' = 'negative',
    'Showing Symptoms But Not Tested,Recovered But Have New Symptoms' = 'negative',
    'Tested Positive,Curious' = 'positive',
    'Tested Positive,Showing Symptoms But Not Tested' = 'positive',
    'Tested Positive,Live With Someone With Coronavirus' = 'positive',
    'Recovered But Have New Symptoms,Curious' = 'negative',
    'Live With Someone With Coronavirus,Self-Isolating With No Symptoms' = 'negative',
    'Tested Positive,Recovered But Have New Symptoms' = 'positive',
    'Live With Someone With Coronavirus,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious' = 'negative',
    'Recovered But Have New Symptoms,Self-Isolating With No Symptoms' = 'negative',
    'Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Tested Positive,Tested Negative But Have Symptoms,Recovered But Have New Symptoms' = 'positive',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Live With Someone With Coronavirus,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'positive',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Curious' = 'positive',
    'Tested Positive,Tested Negative But Have Symptoms' = 'positive',
    'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Showing Symptoms But Not Tested,Live With Someone With Coronavirus' = 'negative',
    'Tested Positive,Recovered But Have New Symptoms,Curious' = 'positive',
    'Tested Negative But Have Symptoms,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Curious'  = 'negative'
  )


data_model <- data_rec %>% 
  dplyr::mutate(Covid_tested = dplyr::recode(tested_or_not, !!!level_key))



data_model<- as.data.frame(data_model)
data_model$Covid_tested <- as.factor(data_model$Covid_tested)

data_model$gender <- as.numeric(data_model$Gender)
data_model$Age <- as.numeric(data_model$Age)
data_model$chills <- as.numeric(data_model$Chills)
data_model$cough  <- as.numeric(data_model$Cough)
data_model$diarrhoea  <- as.numeric(data_model$Diarrhoea)
data_model$fatigue  <- as.numeric(data_model$Fatigue)
data_model$headache   <- as.numeric(data_model$Headcahe)
data_model$loss_smell_taste   <- as.numeric(data_model$Loss.of.smell.and.taste)
data_model$muscle_ache  <- as.numeric(data_model$Muscle.Ache)

data_model$nasal_congestion <- as.numeric(data_model$Nasal.Congestion)

data_model$nausea_vomiting  <- as.numeric(data_model$Nausea.and.Vomiting)

data_model$self_diagnosis <- as.numeric(data_model$Self.Diagnosis)
data_model$shortness_breath <- as.numeric(data_model$Shortness.of.Breath)

data_model$sore_throat <- as.numeric(data_model$Sore.Throat)

data_model$sputum <- as.numeric(data_model$Sputum)

data_model$temperature  <- as.numeric(data_model$Temperature)
data_model$Asthma   <- as.numeric(data_model$`Asthma (managed with an inhaler)`)

data_model$diabetes_type_two <- as.numeric(data_model$`Diabetes Type 2`)
data_model$obesity <- as.numeric(data_model$Obesity)

data_model$hypertension  <- as.numeric(data_model$`High Blood Pressure (hypertension)`)
data_model$heart_disease  <- as.numeric(data_model$`Long-Standing Heart Disease`)

data_model$kidney_disease <- as.numeric(data_model$`Long-Standing Kidney Disease`)

data_model$lung_condition <- as.numeric(data_model$`Long-Standing Lung Condition`)

data_model$liver_disease <- as.numeric(data_model$`Long-Standing Liver Disease`)

data_model$diabetes_type_one <- as.numeric(data_model$`Diabetes Type 1 (controlled by insulin)`)





##################################################################
############### Rename the categories in different variables #####
##################################################################
level_key <-
  c(
    None = 'negative',
    Curious = "negative",
    'Showing Symptoms But Not Tested,Curious' = "negative",
    'Showing Symptoms But Not Tested' = "negative",
    'Self-Isolating With No Symptoms' = "negative",
    'Showing Symptoms But Not Tested,Curious,Self-Isolating With No Symptoms' = "negative",
    'Tested Positive' = 'positive',
    'Curious,Self-Isolating With No Symptoms' = 'negative',
    'Tested Negative But Have Symptoms' = 'negative',
    'Recovered But Have New Symptoms' = 'positive',
    'Live With Someone With Coronavirus' = 'positive',
    'Live With Someone With Coronavirus,Curious' = 'negative',
    'Tested Negative But Have Symptoms,Self-Isolating With No Symptoms' = 'negative',
    'Tested Negative But Have Symptoms,Curious' = 'negative',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested' = 'positive',
    'Tested Positive,Self-Isolating With No Symptoms' = 'positive',
    'Showing Symptoms But Not Tested,Self-Isolating With No Symptoms' = 'negative',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'positive',
    'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested' = 'negative',
    'Showing Symptoms But Not Tested,Recovered But Have New Symptoms' = 'negative',
    'Tested Positive,Curious' = 'positive',
    'Tested Positive,Showing Symptoms But Not Tested' = 'positive',
    'Tested Positive,Live With Someone With Coronavirus' = 'positive',
    'Recovered But Have New Symptoms,Curious' = 'negative',
    'Live With Someone With Coronavirus,Self-Isolating With No Symptoms' = 'negative',
    'Tested Positive,Recovered But Have New Symptoms' = 'positive',
    'Live With Someone With Coronavirus,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious' = 'negative',
    'Recovered But Have New Symptoms,Self-Isolating With No Symptoms' = 'negative',
    'Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Tested Positive,Tested Negative But Have Symptoms,Recovered But Have New Symptoms' = 'positive',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Live With Someone With Coronavirus,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'positive',
    'Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Curious' = 'positive',
    'Tested Positive,Tested Negative But Have Symptoms' = 'positive',
    'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Showing Symptoms But Not Tested,Live With Someone With Coronavirus' = 'negative',
    'Tested Positive,Recovered But Have New Symptoms,Curious' = 'positive',
    'Tested Negative But Have Symptoms,Curious,Self-Isolating With No Symptoms' = 'negative',
    'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Curious'  = 'negative'
  )



write.csv(data_final_numeric, file = "/Users/gabrielburcea/Rprojects/data/data_final_numeric.csv", row.names = FALSE)