In gabrielburcea/cvindia: Analysis of symptoms

library(tidymodels)
library(readr)
library(dplyr)
library(corrr)
library(tidyverse)
library(conflicted)
library(tidymodels)
library(ggrepel)
library(corrplot)
library(dplyr)
library(corrr) 
library(themis)
library(rsample)
library(caret)
library(forcats)
library(rcompanion)
library(MASS)
library(pROC)
library(ROCR)
library(data.table)
library(ggplot2)
library(tidyverse)
library(rms)


conflict_prefer("step", "stats")

data_categ_no_sev <- readr::read_csv("/Users/gabrielburcea/Rprojects/data/data_no_sev_stats.csv")


data_categ_no_sev$gender <- as.factor(data_categ_no_sev$gender)
data_categ_no_sev$country <- as.factor(data_categ_no_sev$country)
data_categ_no_sev$chills <- as.factor(data_categ_no_sev$chills)
data_categ_no_sev$cough  <- as.factor(data_categ_no_sev$cough)
data_categ_no_sev$diarrhoea  <- as.factor(data_categ_no_sev$diarrhoea)
data_categ_no_sev$fatigue  <- as.factor(data_categ_no_sev$fatigue)
data_categ_no_sev$headache   <- as.factor(data_categ_no_sev$headache)
data_categ_no_sev$loss_smell_taste   <- as.factor(data_categ_no_sev$loss_smell_taste)
data_categ_no_sev$muscle_ache  <- as.factor(data_categ_no_sev$muscle_ache)
data_categ_no_sev$nasal_congestion <- as.factor(data_categ_no_sev$nasal_congestion)
data_categ_no_sev$nausea_vomiting  <- as.factor(data_categ_no_sev$nausea_vomiting)
data_categ_no_sev$self_diagnosis <- as.factor(data_categ_no_sev$self_diagnosis)
data_categ_no_sev$shortness_breath <- as.factor(data_categ_no_sev$shortness_breath)
data_categ_no_sev$sore_throat <- as.factor(data_categ_no_sev$sore_throat)
data_categ_no_sev$sputum <- as.factor(data_categ_no_sev$sputum)
data_categ_no_sev$temperature  <- as.factor(data_categ_no_sev$temperature)
data_categ_no_sev$health_care_worker <- as.factor(data_categ_no_sev$health_care_worker)
data_categ_no_sev$care_home_worker <- as.factor(data_categ_no_sev$care_home_worker)

data_categ_no_sev$asthma   <- as.factor(data_categ_no_sev$asthma)
data_categ_no_sev$diabetes_type_two <- as.factor(data_categ_no_sev$diabetes_type_two)
data_categ_no_sev$obesity <- as.factor(data_categ_no_sev$obesity)
data_categ_no_sev$hypertension  <- as.factor(data_categ_no_sev$hypertension)
data_categ_no_sev$heart_disease  <- as.factor(data_categ_no_sev$heart_disease)
data_categ_no_sev$kidney_disease <- as.factor(data_categ_no_sev$kidney_disease)
data_categ_no_sev$lung_condition <- as.factor(data_categ_no_sev$lung_condition)
data_categ_no_sev$liver_disease <- as.factor(data_categ_no_sev$liver_disease)
data_categ_no_sev$diabetes_type_one <- as.factor(data_categ_no_sev$diabetes_type_one)
data_categ_no_sev$how_unwell <- as.factor(data_categ_no_sev$how_unwell)
data_categ_no_sev$age <- as.factor(data_categ_no_sev$age)
data_categ_no_sev$covid_tested <- as.factor(data_categ_no_sev$covid_tested)

asthma_data <- data_categ_no_sev %>%
  dplyr::select(asthma, diabetes_type_one, diabetes_type_two, obesity, hypertension, heart_disease, lung_condition, 
                liver_disease, kidney_disease, gender, age, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature) %>%
  tidyr::drop_na()

Asthma

Univariate analysis

Unvivariate analysis reveal chills, cough, diarrhea, headache, muschle ache, sore throat, nausea and vomiting, shortness of breath, sputum, temperature are the associated Covid symptoms in respondents with asthma.

Asthma and chills

asthma_chills <- glm(asthma ~ chills, data = asthma_data, family = binomial)

summary(asthma_chills)


coef_asthma_chills <- coef(asthma_chills)

# odd ratios 
odd_ratios_ob_ch <- (exp(coef_asthma_chills)-1)*100
odd_ratios_ob_ch

Asthma and cough

asthma_cough <- glm(asthma ~ cough, data = asthma_data, family = binomial)

summary(asthma_cough)


coef_asthma_cough <- coef(asthma_cough)

odd_ratios_ob_co <- (exp(coef_asthma_cough)-1)*100

odd_ratios_ob_co

Asthma and diarrhea

asthma_diarrhea <- glm(asthma ~ diarrhoea, data = asthma_data, family = binomial)

summary(asthma_diarrhea)


# get coef
coef_ob_diarrhea <- coef(asthma_diarrhea)

# odd ratios
odd_ratio_ob_diar <- (exp(coef_ob_diarrhea)-1)*100

odd_ratio_ob_diar

Asthma and headache

asthma_headache <- glm(asthma ~ headache, data = asthma_data, family = binomial)

summary(asthma_headache)

coef_ob_head <- coef(asthma_headache)

odd_ratio_ob_head <- (exp(coef_ob_head)-1)*100

odd_ratio_ob_head

Asthma and loss of smell and taste

asthma_loss_smell <- glm(asthma ~ loss_smell_taste, data = asthma_data, family = binomial)


summary(asthma_loss_smell)

coef_ob_loss_smell <- coef(asthma_loss_smell)

odd_ratio_ob_los <- (exp(coef_ob_loss_smell)-1)*100

odd_ratio_ob_los

Asthma and muscle ache

asthma_muscle_ache <- glm(asthma ~ muscle_ache, data = asthma_data, family = binomial)

summary(asthma_muscle_ache)

coef_ob_muscle_ac <- coef(asthma_muscle_ache)

odd_ratio_ob_los <- (exp(coef_ob_muscle_ac)-1)*100

odd_ratio_ob_los

Asthma and nasal congestion

asthma_nasal_cong <- glm(asthma ~ nasal_congestion, data = asthma_data, family = binomial)

summary(asthma_nasal_cong)


coef_ob_nas_cong <- coef(asthma_nasal_cong)

odd_ratio_ob_nas_cong <- (exp(coef_ob_nas_cong))

odd_ratio_ob_nas_cong

Athma and nausea and vomiting

asthma_nausea_vomitting <- glm(asthma ~ nausea_vomiting, data = asthma_data, family = binomial)

summary(asthma_nausea_vomitting)


coef_ob_naus_vom <- coef(asthma_nausea_vomitting)

odd_ratio_ob_naus_vom <- (exp(coef_ob_naus_vom)-1)*100

odd_ratio_ob_naus_vom

Asthma and shortness of breath

asthma_short_breath <- glm(asthma ~ shortness_breath, data = asthma_data, family = binomial)

summary(asthma_short_breath)

coef_ob_sh_br <- coef(asthma_short_breath)


odd_ratio_ob_sh_br <- (exp(coef_ob_sh_br)-1)*100

odd_ratio_ob_sh_br

Asthma and sore throat

asthma_sore_thr <- glm(asthma ~ sore_throat, data = asthma_data, family = binomial)

summary(asthma_sore_thr)

coef_ob_sore_thr <- coef(asthma_sore_thr)


odd_ratio_ob_sore_thr <- (exp(coef_ob_sore_thr)-1)*100

odd_ratio_ob_sore_thr

Asthma and sputum

asthma_sputum <- glm(asthma ~ sputum, data = asthma_data, family = binomial)


summary(asthma_sputum)


coef_ob_sp <- coef(asthma_sputum)

odd_ratio_ob_sp <- (exp(coef_ob_sp)-1)*100

odd_ratio_ob_sp


vif(asthma_sputum)

Asthma and temperature

asthma_temperature <- glm(asthma ~ temperature, data = asthma_data, family = binomial)


summary(asthma_temperature)

coef_ob_temp <- coef(asthma_temperature)

odd_ratio_ob_temp <- (exp(coef_ob_temp)-1)*100

odd_ratio_ob_temp

vif(asthma_temperature)

Multivariable Logistic Regression

Adding all symptoms that showed to be associated in asthma patients.

When adjusting for all variables, patients showing covid-19 symptoms/of patients with positive covid test, the results show strong evidence for an association between variables such as chills, nausea and vomiting, shortness of breath and temperature (38.1-39; 39.1-40) (p ≤ 0.05) in patients with asthma.

When adjusting for all variables,in patients showing covid-19 symptoms/of patients with positive covid test, in patients with asthma there was:

160 % increase in shortness of breath compared to those who do not suffer of asthma
35 % increase in sputum
107 % increase in 39.1-41 temperature compared to those who do not suffer of asthma
1 % increase in male patients compared to those at the baseline
1 % increase in age compared

asthma_model <- glm(asthma ~ chills + cough + diarrhoea + headache + muscle_ache + nausea_vomiting 
                    + shortness_breath + sputum + temperature, data = asthma_data, family = binomial)

summary(asthma_model)

coef_asthma_model <- coef(asthma_model)

odd_ratio_asthma <- (exp(coef_asthma_model)-1)*100

odd_ratio_asthma

vif(asthma_model)

coef_ob_asthma <- coef(asthma_model)
# Confidence intervals 
confint(asthma_model)

#Put the coefficients and confidence intervals onto a useful scale

conf_int_ast <- exp(confint(asthma_model)) 
conf_int_ast