In gabrielburcea/cvindia: Analysis of symptoms

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = FALSE,
  warning = FALSE,
  message = FALSE
)

library(magrittr)

II. Association analysis.

Second stage of analysis attempts to analyze whether there are difference in Covid-19 symptom manifestation in different comorbidity groups. As mentioned above, I am stratifying respondents with showing symptoms and those who tested positive. Yet, before we go into actual analysis, correlation of variables is undertaken next.

With the first step being achieved, second step focuses on whether there are differences in Covid-19 symptom in different comorbidity groups. Univariate analysis and multivariate logistic regression has aid the second stage analysis. Before the actual analysis it is worth having a look on how I've stratified the patients for the study.

For the second part, in order to reach the goal of this study, I have stratified patients into two different groups. Patients who showed symptoms but haven't been tested and patients that have been Covid tested positive. The rest of respondents were filtered out of the dataset as this group isn't a relevant group. With the stratification in place, we've got from 60812 respondents, with the stratification of patients, I've got to 9436 respondents. Nevertheless, 8752 are showing symptoms whilst those tested are 707. The groups were recoded into tested and not tested. It is worth mentioning on the class imbalance in this dataset.

library(tidyverse)

data_categ_nosev <- readr::read_csv("/Users/gabrielburcea/Rprojects/stats_data_whole/data_categ_nosev_comorbidity_one.csv")


# data_categ_nosev <- data_categ_nosev %>%
#   dplyr::mutate(covid_tested = forcats::fct_recode(covid_tested, !!!level_covid_tested))

count_covid_st <- data_categ_nosev %>%
  dplyr::select(id, covid_tested) %>%
  dplyr::group_by(covid_tested) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percent = n/sum(n)*100)

data_categ_nosev %>% dplyr::distinct(sneezing)

level_gender <- c("Other" = "Gender")

data_categ_nosev <- data_categ_nosev %>%
  dplyr::mutate(gender = fct_recode(gender, !!!level_gender))

data_categ_nosev %>% distinct(gender)

count_gender <- data_categ_nosev %>%
  dplyr::group_by(gender) %>%
  dplyr::summarise(Count = n()) %>%
  dplyr::mutate(Frequency = Count/sum(Count)*100)

data_categ_nosev <- data_categ_nosev %>%
  dplyr::mutate(age_band = dplyr::case_when(
    age == 0 | age <= 20 ~ '0-20',
    age == 21 | age <= 30 ~ '21-30',
    age == 31 | age <= 40 ~ '31-40',
    age == 41 | age <= 50 ~ '41-50',
    age == 51 | age <= 60 ~ '51-60',
    age == 61 | age <= 70 ~ '61-70',
    age == 71 | age <= 80 ~ '71-80',
    age == 81 | age <= 90 ~ '81-100'))

count_age <- data_categ_nosev %>%
  dplyr::group_by(age_band) %>%
  dplyr::summarise(Count = n()) %>%
  dplyr::mutate(Frequency = Count/sum(Count)*100)

as.data.frame(count_age)

knitr::kable(count_age)

data_categ_nosev <- dplyr::mutate(data_categ_nosev, 
                            n_cmdt =  ifelse(number_morbidities %in% 0 , "no morbidity", 
                                      ifelse(number_morbidities %in% 1, "1 morbidity", 
                                      ifelse(number_morbidities %in% 2 , "2 comorbidities",        
                                      ifelse(number_morbidities %in% 3:99, ">3 comorbidites", NA))))) %>%
  dplyr::filter(n_cmdt != "no morbidity")

data_categ_nosev$number_morbidities <- as.factor(data_categ_nosev$number_morbidities)

count_comorbidities <- data_categ %>%
  dplyr::group_by(n_cmdt) %>%
  tally() %>%
  dplyr::mutate(Frequency = n/sum(n) *100)


level_covid_tested <- c("positive" = "Tested Positive,Self-Isolating With No Symptoms",
                        "positive" = "Tested Positive,Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms")

data_categ_covid <- data_categ_nosev %>%
  dplyr::filter(covid_tested != 'none') %>%
  dplyr::mutate(status_cv = dplyr::case_when(covid_tested == 'showing symptoms' ~ 0,
                                             covid_tested == 'positive' ~ 1)) %>%
  tidyr::drop_na()

How many male and female we have in our dataset? There are 5083 male accounting for 53 percent whilst female are 4321 accounting for 45 percent. Also, we have very low percent of other group.

gender_tb <- data_categ_covid %>%
  dplyr::select(id, gender) %>%
  dplyr::group_by(gender) %>%
  dplyr::tally() %>%
  dplyr::mutate(percent = n/sum(n))

gender_tb

bp <- ggplot2::ggplot(gender_tb, ggplot2::aes(x = "", y = percent, fill = gender)) + 
  ggplot2::geom_bar(width = 1, stat = "identity")

pie <- bp + ggplot2::coord_polar("y", start = 0) + 
  ggplot2::scale_fill_brewer(palette = "Blues") +
  ggplot2::theme(axis.text.x = ggplot2::element_blank())

pie

library(report)

# data_categ_nosev <- data_categ_nosev %>%
#   dplyr::filter(covid_tested != 'none') %>%
#   dplyr::mutate(status_cv = dplyr::case_when(
#                                              covid_tested == 'showing symptoms' ~ 0,
#                                              covid_tested == 'positive' ~ 1), 
#                 number_comorbidities = dplyr::case_when(number_morbidities == 1 ~ 'one', 
#                                                         number_morbidities >= 2 ~ 'more than 2')) %>%
#   
#   tidyr::drop_na()
# 
# data_categ_nosev <- data_categ_nosev %>% dplyr::rename(id = ID, covid_tested = Covid_tested, gender = Gender, age = Age)

show_sympt_positive <- data_categ_covid %>%
  dplyr::select(id, status_cv) %>%
  dplyr::group_by(status_cv) %>%
  dplyr::tally()

knitr::kable(show_sympt_positive)

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(qgraph)
library(report)
library(corrplot)

conflict_prefer("step", "stats")

### ML for Mixed - categorical and numerica data ####

Correlations

Correlations matrix is done on numerical variables. However, I have transformed the categorical variables into numerical ones, as I cannot correlate all categorical variables once. Additionally, the correlation is done on original dataset and not on the 9436 datasets since a lot of respondents that declared they have no covid have reported some covid symptoms. However, this has to be discussed more in detail and wait for a bigger dataset.

From the correlation matrix, it is noticed, fatigue and muscle ache seem to be correlated, but only with 0.43550, the highest correlation. Yet, for the highest correlation, it is not even passing the 0.5. However, I choose to take out of the analysis the fatigue variable.

###################################
#######Corelations ################


data_cor <- data_categ_nosev
data_cor <- data_categ_nosev %>%
  dplyr::select(chills, cough, diarrhoea, fatigue, headache, loss_smell_taste, muscle_ache, nasal_congestion, 
         nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, loss_appetite, chest_pain, itchy_eyes, 
         joint_pain, asthma, diabetes_type_one, diabetes_type_two, obesity, hypertension, heart_disease, lung_condition, liver_disease, 
         kidney_disease)

correlations <- cor_auto(data_cor)


corrplot(correlations, type = "upper", order = "hclust", tl.col = "black", tl.srt = 45)

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_covid$id <- NULL 
data_categ_nosev$country <- NULL
data_categ_covid$location <- NULL
data_categ_covid$date_completed <- NULL
data_categ_covid$covid_tested <- NULL 
data_categ_covid$age_band <- NULL
data_categ_covid$status_cv <- NULL
data_categ_covid$sneezing <- NULL


###########################################################################################
### Transforming variables in factor format ###############################################
#data_categ_covid$country <- as.factor(data_categ_covid$country)
data_categ_covid$chills <- as.factor(data_categ_covid$chills)
data_categ_covid$cough  <- as.factor(data_categ_covid$cough)
data_categ_covid$gender <- as.factor(data_categ_covid$gender)
#data_categ_covid$covid_tested <- as.factor(data_categ_covid$covid_tested)
data_categ_covid$diarrhoea  <- as.factor(data_categ_covid$diarrhoea)
data_categ_covid$fatigue  <- as.factor(data_categ_covid$fatigue)
data_categ_covid$headache   <- as.factor(data_categ_covid$headache)
data_categ_covid$loss_smell_taste   <- as.factor(data_categ_covid$loss_smell_taste)
data_categ_covid$muscle_ache  <- as.factor(data_categ_covid$muscle_ache)
data_categ_covid$nasal_congestion <- as.factor(data_categ_covid$nasal_congestion)
data_categ_covid$nausea_vomiting  <- as.factor(data_categ_covid$nausea_vomiting)
data_categ_covid$self_diagnosis <- as.factor(data_categ_covid$self_diagnosis)
data_categ_covid$shortness_breath <- as.factor(data_categ_covid$shortness_breath)
data_categ_covid$sore_throat <- as.factor(data_categ_covid$sore_throat)
data_categ_covid$sputum <- as.factor(data_categ_covid$sputum)
data_categ_covid$temperature  <- as.factor(data_categ_covid$temperature)
data_categ_covid$loss_appetite <- as.factor(data_categ_covid$loss_appetite)
data_categ_covid$chest_pain <- as.factor(data_categ_covid$chest_pain)
data_categ_covid$itchy_eyes <- as.factor(data_categ_covid$itchy_eyes)
data_categ_covid$joint_pain <- as.factor(data_categ_covid$joint_pain)


### Transforming variables in numerical format  #########################################################
data_categ_covid$asthma   <- as.factor(data_categ_covid$asthma)
data_categ_covid$diabetes_type_two <- as.factor(data_categ_covid$diabetes_type_two)
data_categ_covid$obesity <- as.factor(data_categ_covid$obesity)
data_categ_covid$hypertension  <- as.factor(data_categ_covid$hypertension)
data_categ_covid$heart_disease  <- as.factor(data_categ_covid$heart_disease)
data_categ_covid$kidney_disease <- as.factor(data_categ_covid$kidney_disease)
data_categ_covid$lung_condition <- as.factor(data_categ_covid$lung_condition)
data_categ_covid$liver_disease <- as.factor(data_categ_covid$liver_disease)
data_categ_covid$diabetes_type_one <- as.factor(data_categ_covid$diabetes_type_one)

data_categ_covid$number_days_symptoms <- as.numeric(data_categ_covid$number_days_symptoms)
data_categ_covid$age <- as.numeric(data_categ_covid$age)

data_categ_covid$temperature <- as.factor(data_categ_nosev$temperature)
#data_categ_nosev$covid_tested <- as.factor(data_categ_nose)

obesity_data <- data_categ_covid %>%
  dplyr::select(id, obesity, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, loss_appetite, chest_pain, itchy_eyes, joint_pain) %>%
  tidyr::drop_na()

obesity_count <- obesity_data %>%
  tidyr::pivot_longer(cols = 3:18, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(obesity == "Yes" & yes_no == "Yes")%>%
  group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Obesity across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_obesity_sympt <-
  ggplot2::ggplot(obesity_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(obesity_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_obesity_sympt

Univariate analysis

Univariate analysis reveal that cough, diarhea, muscle ache, nausea and vomiting, sputum, temperature are associated factors in obese patients.

obesity_data <- obesity_data %>%
  dplyr::select(-id)

obesity_data$obesity <- as.factor(obesity_data$obesity)
obesity_chills <- glm(obesity ~ chills, data = obesity_data, family = binomial)

summary(obesity_chills)

coef_obesity_chills <- coef(obesity_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_obesity_chills)
odd_ratios_ob_ch

obesity_cough <- glm(obesity ~ cough, data = obesity_data, family = binomial)

summary(obesity_cough)


coef_obesity_cough <- coef(obesity_cough)

odd_ratios_ob_co <- exp(coef_obesity_cough)

odd_ratios_ob_co

obesity_diarrhea <- glm(obesity ~ diarrhoea, data = obesity_data, family = binomial)

summary(obesity_diarrhea)


# get coef
coef_ob_diarrhea <- coef(obesity_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

obesity_headache <- glm(obesity ~ headache, data = obesity_data, family = binomial)

summary(obesity_headache)

coef_ob_head <- coef(obesity_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

obesity_loss_smell <- glm(obesity ~ loss_smell_taste, data = obesity_data, family = binomial)


summary(obesity_loss_smell)



coef_ob_loss_smell <- coef(obesity_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

library(fmsb)

obesity_muscle_ache <- glm(obesity ~ muscle_ache, data = obesity_data, family = binomial)

summary(obesity_muscle_ache)




coef_ob_muscle_ac <- coef(obesity_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

obesity_nasal_cong <- glm(obesity ~ nasal_congestion, data = obesity_data, family = binomial)

summary(obesity_nasal_cong)


coef_ob_nas_cong <- coef(obesity_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

obesity_nausea_vomitting <- glm(obesity ~ nausea_vomiting, data = obesity_data, family = binomial)

summary(obesity_nausea_vomitting)


coef_ob_naus_vom <- coef(obesity_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

obesity_short_breath <- glm(obesity ~ shortness_breath, data = obesity_data, family = binomial)

summary(obesity_short_breath)

coef_ob_sh_br <- coef(obesity_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

obesity_sore_thr <- glm(obesity ~ sore_throat, data = obesity_data, family = binomial)

summary(obesity_sore_thr)

coef_ob_sore_thr <- coef(obesity_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

obesity_sputum <- glm(obesity ~ sputum, data = obesity_data, family = binomial)


summary(obesity_sputum)


coef_ob_sp <- coef(obesity_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(obesity_sputum)

obesity_temperature <- glm(obesity ~ temperature, data = obesity_data, family = binomial)


summary(obesity_temperature)

coef_ob_temp <- coef(obesity_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(obesity_temperature)

obesity_itchy_eyes <- glm(obesity ~ itchy_eyes, data = obesity_data, family = binomial)

summary(obesity_itchy_eyes)

coef_ob_itchy <- coef(obesity_itchy_eyes)

odd_ratio_ob_itchy <- exp(coef_ob_itchy)

odd_ratio_ob_itchy

vif(obesity_itchy_eyes)

obesity_chest_pain <- glm(obesity ~ chest_pain, data = obesity_data, family = binomial)

summary(obesity_chest_pain)

obesity_loss_appetite <- glm(obesity ~ loss_appetite, data = obesity_data, family = binomial)

summary(obesity_loss_appetite)

obesity_joint_pain <- glm(obesity ~ joint_pain, data = obesity_data, family = binomial)


summary(obesity_joint_pain)

Adding all variables that showed an association with obesity.

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 cough, diarrhea, sputum and temperature (37.5-38) (p ≤ 0.05) in obese respondents. When adjusting for all variables,in patients showing covid-19 symptpms/of patients with positive covid test, in obese respondents there was: - 15 % increase in odds of experiencing cough compared to those who aren't obese - 35 % increase in diarrhea compared to those who aren't obese - 23 % increase in soutum compared to those who aren't obese - 24 % decrease ??? in 37.5-38 temperature compared to those who do not suffer of heart disease

obesity_model <- glm(obesity ~ cough + diarrhoea + shortness_breath + temperature + loss_smell_taste + headache + muscle_ache + nasal_congestion + itchy_eyes + loss_appetite,  data = obesity_data, family = binomial)

summary(obesity_model)


# odds ratio and 95% CL

knitr::kable(exp(cbind(OR = coef(obesity_model), confint(obesity_model))))

asthma_count <- asthma_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(asthma == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Asthma across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_asthma_sympt <-
  ggplot2::ggplot(asthma_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(asthma_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_asthma_sympt

asthma_data <- data_categ_nosev %>%
  dplyr::select(asthma, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, loss_appetite, chest_pain, itchy_eyes, joint_pain) %>%
  tidyr::drop_na()

Univariate analysis for asthma

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)
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)

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)

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)

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)

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)

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)

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)

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)

odd_ratio_ob_sp


vif(asthma_sputum)

Asthma and temperature

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

summary(asthma_temperature)

asthma_itchy <- glm(asthma ~ itchy_eyes, data = asthma_data, family = binomial)

summary(asthma_temperature)

asthma_joint_pain <- glm(asthma ~ joint_pain, data = asthma_data, family = binomial)

summary(asthma_joint_pain)

asthma_chest_pain <- glm(asthma ~ chest_pain, data = asthma_data, family = binomial)

summary(asthma_chest_pain)

asthma_loss_appetite <- glm(asthma ~ loss_appetite, data = asthma_data, family = binomial)


summary(asthma_loss_appetite)

Multivariable Logistic Regression for Asthma

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

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 + loss_smell_taste + nasal_congestion + sore_throat + itchy_eyes + joint_pain + chest_pain, data = asthma_data, family = binomial)

summary(asthma_model)

Odd Ratios and 95 % CL for Asthma model

# odds ratios and 95% CL

knitr::kable(exp(cbind(OR = coef(asthma_model), confint(asthma_model))))

diabetes_type_one_data <- data_categ_nosev %>%
  dplyr::select(diabetes_type_one, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, joint_pain, itchy_eyes, chest_pain, loss_appetite) %>%
  tidyr::drop_na()

diabetes_count <- diabetes_type_one_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(diabetes_type_one == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Diabetes type one across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_diabetes_sympt <-
  ggplot2::ggplot(diabetes_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(diabetes_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_diabetes_sympt

Univariate analysis for diabetes type one

The univariate analysis real that symptoms such as headaches, nasal congestion, sore throat, temperature (39.1-41) are associated with diabetes type one.

diabetes_type_one_chills <- glm(diabetes_type_one ~ chills, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_chills)


coef_diabetes_type_one_chills <- coef(diabetes_type_one_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_diabetes_type_one_chills)
odd_ratios_ob_ch

Diabetes type one with cough

diabetes_type_one_cough <- glm(diabetes_type_one ~ cough, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_cough)


coef_diabetes_type_one_cough <- coef(diabetes_type_one_cough)

odd_ratios_ob_co <- exp(coef_diabetes_type_one_cough)

odd_ratios_ob_co

Diabetes type one with diarrhea

diabetes_type_one_diarrhea <- glm(diabetes_type_one ~ diarrhoea, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_diarrhea)


# get coef
coef_ob_diarrhea <- coef(diabetes_type_one_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

Diabetes type one with headache

diabetes_type_one_headache <- glm(diabetes_type_one ~ headache, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_headache)

coef_ob_head <- coef(diabetes_type_one_headache)

odd_ratio_ob_head <- exp(coef_ob_head)
odd_ratio_ob_head

Diabetes type one with loss of smell and taste

diabetes_type_one_loss_smell <- glm(diabetes_type_one ~ loss_smell_taste, data = diabetes_type_one_data, family = binomial)


summary(diabetes_type_one_loss_smell)

coef_ob_loss_smell <- coef(diabetes_type_one_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

Diabetes type one with with muscle ache

diabetes_type_one_muscle_ache <- glm(diabetes_type_one ~ muscle_ache, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_muscle_ache)

coef_ob_muscle_ac <- coef(diabetes_type_one_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

Diabetes type one with nasal congestion

diabetes_type_one_nasal_cong <- glm(diabetes_type_one ~ nasal_congestion, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_nasal_cong)


coef_ob_nas_cong <- coef(diabetes_type_one_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

Diabetes type one with nausea and vomiting

diabetes_type_one_nausea_vomitting <- glm(diabetes_type_one ~ nausea_vomiting, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_nausea_vomitting)


coef_ob_naus_vom <- coef(diabetes_type_one_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

Diabetest type one with shortness of breath

diabetes_type_one_short_breath <- glm(diabetes_type_one ~ shortness_breath, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_short_breath)

coef_ob_sh_br <- coef(diabetes_type_one_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

Diabetes type one with sore throat

diabetes_type_one_sore_thr <- glm(diabetes_type_one ~ sore_throat, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_sore_thr)

coef_ob_sore_thr <- coef(diabetes_type_one_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

Diabetes type one with sputum

diabetes_type_one_sputum <- glm(diabetes_type_one ~ sputum, data = diabetes_type_one_data, family = binomial)


summary(diabetes_type_one_sputum)


coef_ob_sp <- coef(diabetes_type_one_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(diabetes_type_one_sputum)

Diabetes type one with temperature

diabetes_type_one_temperature <- glm(diabetes_type_one ~ temperature, data = diabetes_type_one_data, family = binomial)


summary(diabetes_type_one_temperature)

coef_ob_temp <- coef(diabetes_type_one_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(diabetes_type_one_temperature)

diab_one_itchy <- glm(diabetes_type_one ~ itchy_eyes, data = diabetes_type_one_data, family = binomial)

summary(diab_one_itchy)

diabetes_one_joint_pain <- glm(diabetes_type_one ~ joint_pain, data = diabetes_type_one_data, family = binomial)

summary(diabetes_one_joint_pain)

diabetes_one_chest_pain <- glm(diabetes_type_one ~ chest_pain, data = diabetes_type_one_data, family = binomial)

summary(diabetes_one_chest_pain)

diabetes_one_loss_appetite <- glm(diabetes_type_one ~ loss_appetite, data = diabetes_type_one_data, family = binomial)


summary(diabetes_one_loss_appetite)

Multivariate analysis for diabetest type one

When adding all variables that showed an association with the heart disease model, the model shows something different.

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 headaches and temperature(39.1-41) (p ≤ 0.01) in patients with diabetes type one.
When adjusting for all variables,in patients showing covid-19 symptpms/of patients with positive covid test, in respondent with diabetes type one there was: - 54 % decrease in odds of experiencing headaches compared to those who do not suffer of diabetes type one - 406 % increase in temperature compared to those who do not suffer of heart disease

diabetes_type_one_model <- glm(diabetes_type_one ~ chills + cough + headache + loss_smell_taste + muscle_ache + nausea_vomiting + shortness_breath + temperature + itchy_eyes + loss_appetite + diarrhoea + nasal_congestion + sore_throat + sputum + joint_pain + chest_pain, data = diabetes_type_one_data, family = binomial)

summary(diabetes_type_one_model)

Odd Ratios and 95 % CL for Diabetes Model

# odds ratio and 95% CL

exp(cbind(OR = coef(diabetes_type_one_model), confint(diabetes_type_one_model)))

vif(diabetes_type_one_model)

diabetes_type_two_data <- data_categ_nosev %>%
  dplyr::select(diabetes_type_two,  chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, joint_pain, chest_pain, itchy_eyes, loss_appetite) %>%
  tidyr::drop_na()

diabetes_two_count <- diabetes_type_two_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(diabetes_type_two == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Diabetes type two across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_diabetes_two_sympt <-
  ggplot2::ggplot(diabetes_two_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(diabetes_two_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_diabetes_two_sympt

Univariate analysis for diabetes type one

Univariate analysis reveal Covid symptoms such as headaches, shortness of breath, sore throat, sputum and temperature are associated wit diabetes type two respondents.

Diabetes type two

diabetes_type_two_chills <- glm(diabetes_type_two ~ chills, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_chills)


coef_diabetes_type_two_chills <- coef(diabetes_type_two_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_diabetes_type_two_chills)
odd_ratios_ob_ch

diabetes_type_two_cough <- glm(diabetes_type_two ~ cough, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_cough)


coef_diabetes_type_two_cough <- coef(diabetes_type_two_cough)

odd_ratios_ob_co <- exp(coef_diabetes_type_two_cough)

odd_ratios_ob_co

diabetes_type_two_diarrhea <- glm(diabetes_type_two ~ diarrhoea, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_diarrhea)


# get coef
coef_ob_diarrhea <- coef(diabetes_type_two_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

diabetes_type_two_headache <- glm(diabetes_type_two ~ headache, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_headache)

coef_ob_head <- coef(diabetes_type_two_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

diabetes_type_two_loss_smell <- glm(diabetes_type_two ~ loss_smell_taste, data = diabetes_type_two_data, family = binomial)


summary(diabetes_type_two_loss_smell)

coef_ob_loss_smell <- coef(diabetes_type_two_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

diabetes_type_two_muscle_ache <- glm(diabetes_type_two ~ muscle_ache, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_muscle_ache)

coef_ob_muscle_ac <- coef(diabetes_type_two_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

diabetes_type_two_nasal_cong <- glm(diabetes_type_two ~ nasal_congestion, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_nasal_cong)


coef_ob_nas_cong <- coef(diabetes_type_two_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

diabetes_type_two_nausea_vomitting <- glm(diabetes_type_two ~ nausea_vomiting, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_nausea_vomitting)


coef_ob_naus_vom <- coef(diabetes_type_two_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

diabetes_type_two_short_breath <- glm(diabetes_type_two ~ shortness_breath, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_short_breath)

coef_ob_sh_br <- coef(diabetes_type_two_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

diabetes_type_two_sore_thr <- glm(diabetes_type_two ~ sore_throat, data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_sore_thr)

coef_ob_sore_thr <- coef(diabetes_type_two_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

diabetes_type_two_sputum <- glm(diabetes_type_two ~ sputum, data = diabetes_type_two_data, family = binomial)


summary(diabetes_type_two_sputum)


coef_ob_sp <- coef(diabetes_type_two_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(diabetes_type_two_sputum)

diabetes_type_two_temperature <- glm(diabetes_type_two ~ temperature, data = diabetes_type_two_data, family = binomial)


summary(diabetes_type_two_temperature)

coef_ob_temp <- coef(diabetes_type_two_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(diabetes_type_two_temperature)

diab_two_itchy <- glm(diabetes_type_one ~ itchy_eyes, data = diabetes_type_one_data, family = binomial)

summary(diab_two_itchy )

diabetes_two_joint_pain <- glm(diabetes_type_one ~ joint_pain, data = diabetes_type_one_data, family = binomial)

summary(diabetes_two_joint_pain)

diabetes_two_chest_pain <- glm(asthma ~ chest_pain, data = asthma_data, family = binomial)

summary(diabetes_two_chest_pain)

diabetes_two_loss_appetite <- glm(asthma ~ loss_appetite, data = asthma_data, family = binomial)


summary(diabetes_two_loss_appetite)

Multivariable analysis for diabetes type two

Adding all variables that showed an association with diabetes type two variable.

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 headache, shortness of breath, sore throat, sputum, temperature age and gender (p ≤ 0.05) in patients with heart disease.
When adjusting for all variables,in patients showing covid-19 symptpms/of patients with positive covid test, in patients with diabetes type two there was: - 26 % decrease in odds of experiencing headaches - 21 % decrease in shortness of breath - 28 % decrease in sputum compared to those who do not suffer of patientss of diabetes type two - 50 % increase in 37.5-38 temperature compared to those who do not suffer of diabetes type two - 87 % increase in 38.1-39 temperature compared to those who do not suffer of diabetes type two - 222 % increase ?? in 39.1-41 temperature - 79 % for gender ?

diabetes_type_two_model <- glm(diabetes_type_two ~ cough + headache + shortness_breath + sore_throat + temperature + nasal_congestion + itchy_eyes + chest_pain, 
                               data = diabetes_type_two_data, family = binomial)

summary(diabetes_type_two_model)

Odd Ratios and 95 % CL for

exp(cbind(OR = coef(diabetes_type_two_model), confint(diabetes_type_two_model)))

vif(diabetes_type_two_model)

heart_data <- data_categ_nosev %>%
  dplyr::select(heart_disease, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, itchy_eyes, chest_pain, loss_appetite, joint_pain) %>%
  tidyr::drop_na()

heart_count <- heart_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(heart_disease == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Heart Disease across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_asthma_sympt <-
  ggplot2::ggplot(heart_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(heart_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_asthma_sympt

Univariate analysis

Univariate analysis reveal Covid symptoms such as chills, loss of smell and taste, diarhoea, muscle ache , nausea and vomiting, shortness of breath, sputum and temperature(39.1-41) are associated with heart disease.

Heart disease and chills

heart_chills <- glm(heart_disease ~ chills, data = heart_data, family = binomial)

summary(heart_chills)


coef_heart_chills <- coef(heart_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_heart_chills)
odd_ratios_ob_ch

Heart disease and cough

heart_cough <- glm(heart_disease ~ cough, data = heart_data, family = binomial)

summary(heart_cough)


coef_heart_cough <- coef(heart_cough)

odd_ratios_ob_co <- exp(coef_heart_cough)

odd_ratios_ob_co

Heart disease and diarrhea

heart_diarrhea <- glm(heart_disease ~ diarrhoea, data = heart_data, family = binomial)

summary(heart_diarrhea)


# get coef
coef_ob_diarrhea <- coef(heart_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

Heart disease and headache

heart_headache <- glm(heart_disease ~ headache, data = heart_data, family = binomial)

summary(heart_headache)

coef_ob_head <- coef(heart_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

Heart disease and loss of smell and taste

heart_loss_smell <- glm(heart_disease ~ loss_smell_taste, data = heart_data, family = binomial)


summary(heart_loss_smell)

coef_ob_loss_smell <- coef(heart_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

Heart disease and muscle ache.

heart_muscle_ache <- glm(heart_disease ~ muscle_ache, data = heart_data, family = binomial)

summary(heart_muscle_ache)

coef_ob_muscle_ac <- coef(heart_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

Heart disease and nasal congestion

heart_nasal_cong <- glm(heart_disease ~ nasal_congestion, data = heart_data, family = binomial)

summary(heart_nasal_cong)


coef_ob_nas_cong <- coef(heart_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

Heart disease and nausea and vomiting

heart_nausea_vomitting <- glm(heart_disease ~ nausea_vomiting, data = heart_data, family = binomial)

summary(heart_nausea_vomitting)


coef_ob_naus_vom <- coef(heart_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

Heart disease and shortness of breath

heart_short_breath <- glm(heart_disease ~ shortness_breath, data = heart_data, family = binomial)

summary(heart_short_breath)

coef_ob_sh_br <- coef(heart_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

Heart disease and sore throat

heart_sore_thr <- glm(heart_disease ~ sore_throat, data = heart_data, family = binomial)

summary(heart_sore_thr)

coef_ob_sore_thr <- coef(heart_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

11.Heart disease and sputum

heart_sputum <- glm(heart_disease ~ sputum, data = heart_data, family = binomial)


summary(heart_sputum)


coef_ob_sp <- coef(heart_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(heart_sputum)

Heart disease and temperature

heart_temperature <- glm(heart_disease ~ temperature, data = heart_data, family = binomial)


summary(heart_temperature)

coef_ob_temp <- coef(heart_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(heart_temperature)

heart_itchy <- glm(heart_disease ~ itchy_eyes, data = heart_data, family = binomial)

summary(heart_itchy)

heart_joint_pain <- glm(heart_disease ~ joint_pain, data = heart_data, family = binomial)

summary(heart_joint_pain)

heart_chest_pain <- glm(heart_disease ~ chest_pain, data = heart_data, family = binomial)

summary(heart_chest_pain)

heart_loss_appetite <- glm(heart_disease ~ loss_appetite, data = heart_data, family = binomial)


summary(heart_loss_appetite)

Multivariate analysis for heart disease

Adding all variables that showed an association with the heart disease model.

When adjusting for all variables,in patients showing covid-19 symptpms/of patients with positive covid test, in patients with heart disease there was: - 94 % increase in odds of experiencing chills compared to those who do not suffer of heart diesease disease - 95 % increase in nausea and vomiting compared to those who do not suffer of heart disease - 44 % increase in shortness of breath compared to those who do not suffer of heart disease - 7 % increase in 37.5-38 temperature compared to those who do not suffer of heart disease - 229 % increase in 39.1-41 temperature

heart_model <- glm(heart_disease ~ chills + cough + muscle_ache + shortness_breath +
                      sputum  + chest_pain, data = heart_data, family = binomial)

summary(heart_model)

exp(cbind(OR = coef(heart_model), confint(heart_model)))

vif(heart_model)

hypertension_data <- data_categ_nosev %>%
  dplyr::select(hypertension,  chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, joint_pain, chest_pain, itchy_eyes, loss_appetite) %>%
  tidyr::drop_na()

hypertension_data$hypertension <- as.factor(hypertension_data$hypertension)

hypertension_count <- hypertension_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(hypertension == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Hypertension across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_hypertension_sympt <-
  ggplot2::ggplot(hypertension_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(hypertension_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_hypertension_sympt

Univariate analysis for hypertension and Covid symptoms

Univariate analysis reveal cough, diarrhea, muscle ache, shortness of breath, sputum and temperature (38.1-39) are symptoms associated in patients with hypertension.

1.Hypertension and chills

hypertension_chills <- glm(hypertension ~ chills, data = hypertension_data, family = binomial)

summary(hypertension_chills)


coef_hypertension_chills <- coef(hypertension_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_hypertension_chills)
odd_ratios_ob_ch

Hypertension and cough

hypertension_cough <- glm(hypertension ~ cough, data = hypertension_data, family = binomial)

summary(hypertension_cough)


coef_hypertension_cough <- coef(hypertension_cough)

odd_ratios_ob_co <- exp(coef_hypertension_cough)

odd_ratios_ob_co

Hypertension and diarrhea

hypertension_diarrhea <- glm(hypertension ~ diarrhoea, data = hypertension_data, family = binomial)

summary(hypertension_diarrhea)


# get coef
coef_ob_diarrhea <- coef(hypertension_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

Hypertension and headache

hypertension_headache <- glm(hypertension ~ headache, data = hypertension_data, family = binomial)

summary(hypertension_headache)

coef_ob_head <- coef(hypertension_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

Hypertension and loss of smell and taste

hypertension_loss_smell <- glm(hypertension ~ loss_smell_taste, data = hypertension_data, family = binomial)


summary(hypertension_loss_smell)

coef_ob_loss_smell <- coef(hypertension_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

Hypertension and muscle ache

hypertension_muscle_ache <- glm(hypertension ~ muscle_ache, data = hypertension_data, family = binomial)

summary(hypertension_muscle_ache)

coef_ob_muscle_ac <- coef(hypertension_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

Hypertension and nasal congestion

hypertension_nasal_cong <- glm(hypertension ~ nasal_congestion, data = hypertension_data, family = binomial)

summary(hypertension_nasal_cong)


coef_ob_nas_cong <- coef(hypertension_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

Hypertension and nausea and vomiting

hypertension_nausea_vomitting <- glm(hypertension ~ nausea_vomiting, data = hypertension_data, family = binomial)

summary(hypertension_nausea_vomitting)


coef_ob_naus_vom <- coef(hypertension_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

Hypertension and shortness of breath

hypertension_short_breath <- glm(hypertension ~ shortness_breath, data = hypertension_data, family = binomial)

summary(hypertension_short_breath)

coef_ob_sh_br <- coef(hypertension_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

Hypertension and sore throat

hypertension_sore_thr <- glm(hypertension ~ sore_throat, data = hypertension_data, family = binomial)

summary(hypertension_sore_thr)

coef_ob_sore_thr <- coef(hypertension_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

Hypertension and sputum

hypertension_sputum <- glm(hypertension ~ sputum, data = hypertension_data, family = binomial)


summary(hypertension_sputum)


coef_ob_sp <- coef(hypertension_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(hypertension_sputum)

Hypertension and temperature

hypertension_temperature <- glm(hypertension ~ temperature, data = hypertension_data, family = binomial)


summary(hypertension_temperature)

coef_ob_temp <- coef(hypertension_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(hypertension_temperature)

hypertension_itchy <- glm(hypertension ~ itchy_eyes, data = hypertension_data, family = binomial)


summary(hypertension_itchy)

hypertension_chest_pain <- glm(hypertension ~ chest_pain, data = hypertension_data, family = binomial)

summary(hypertension_chest_pain)

hypertension_loss_appetite <-glm(hypertension ~ loss_appetite, data = hypertension_data, family = binomial)

summary(hypertension_loss_appetite)

hypertension_joint_pain<-glm(hypertension ~ joint_pain, data = hypertension_data, family = binomial)

summary(hypertension_joint_pain)

Multivariable analysis for hypertension

Adding all variables that showed an association with the hypertension variable.

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 cough, muscle ache, shortness of breath, sputum and temperature (37.1- 38 ; 38.1-39) (p ≤ 0.05) in patients with hypertension.
When adjusting for all variables,in patients showing covid-19 symptpms/of patients with positive covid test, in patients with hypertension there was: - 24 % increase in odds of experiencing cough compared to those who do not suffer of hypertension - 15 % increase in diarrhea compared to those who do not suffer of hypertension - 12 % increase in muscle ache compared to those who do not suffer of hypertension - 5 % increase in sputum compared to those who do not suffer of hypertension - 51 % increase in 38.1-39 in temperature to those who do not suffer of hypertension - 21 % increase in 39.1-41 in temperature compared to those who do not suffer of hypertension

cough, diarrhea, muscle ache, shortness of breath, sputum, temperature

hypertension_model <- glm(hypertension ~ cough + diarrhoea + headache + loss_smell_taste + nasal_congestion + muscle_ache + shortness_breath + joint_pain + temperature + loss_appetite,  data = hypertension_data, family = binomial)

summary(hypertension_model)

exp(cbind(OR = coef(hypertension_model), confint(hypertension_model)))

vif(hypertension_model)

liver_data <- data_categ_nosev %>%
  dplyr::select(liver_disease, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, joint_pain, itchy_eyes, chest_pain, loss_appetite) %>%
  tidyr::drop_na()

liver_count <- liver_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(liver_disease == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Liver disease across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_liver_sympt <-
  ggplot2::ggplot(liver_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(liver_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_liver_sympt

Univariate analysis for liver disease and Covid-19 symptoms

Asociated Covid symptoms in respondents with liver disease are: chills, diarhoea, loss of smell and taste, muscle ache, nasal congestion, nausea and vomiting, sputum and temperature

Liver disease and chills

liver_chills <- glm(liver_disease ~ chills, data = liver_data, family = binomial)

summary(liver_chills)


coef_liver_chills <- coef(liver_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_liver_chills)
odd_ratios_ob_ch

Liver disease and cough

liver_cough <- glm(liver_disease ~ cough, data = liver_data, family = binomial)

summary(liver_cough)


coef_liver_cough <- coef(liver_cough)

odd_ratios_ob_co <- exp(coef_liver_cough)

odd_ratios_ob_co

Liver disease and diarhoea

liver_diarrhea <- glm(liver_disease ~ diarrhoea, data = liver_data, family = binomial)

summary(liver_diarrhea)


# get coef
coef_ob_diarrhea <- coef(liver_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

Liver disease and headache

liver_headache <- glm(liver_disease ~ headache, data = liver_data, family = binomial)

summary(liver_headache)

coef_ob_head <- coef(liver_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

Liver disease and loss of smell and taste

liver_loss_smell <- glm(liver_disease ~ loss_smell_taste, data = liver_data, family = binomial)


summary(liver_loss_smell)

coef_ob_loss_smell <- coef(liver_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

Liver disease and muscle ache

liver_muscle_ache <- glm(liver_disease ~ muscle_ache, data = liver_data, family = binomial)

summary(liver_muscle_ache)

coef_ob_muscle_ac <- coef(liver_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

Liver disease and nasal congestion

liver_nasal_cong <- glm(liver_disease ~ nasal_congestion, data = liver_data, family = binomial)

summary(liver_nasal_cong)


coef_ob_nas_cong <- coef(liver_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

Liver disease and vomiting

liver_nausea_vomitting <- glm(liver_disease ~ nausea_vomiting, data = liver_data, family = binomial)

summary(liver_nausea_vomitting)


coef_ob_naus_vom <- coef(liver_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

Liver disease and shortness of breath

liver_short_breath <- glm(liver_disease ~ shortness_breath, data = liver_data, family = binomial)

summary(liver_short_breath)

coef_ob_sh_br <- coef(liver_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

Liver disease and sore throat

liver_sore_thr <- glm(liver_disease ~ sore_throat, data = liver_data, family = binomial)

summary(liver_sore_thr)

coef_ob_sore_thr <- coef(liver_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

Liver disease and sputum

liver_sputum <- glm(liver_disease ~ sputum, data = liver_data, family = binomial)


summary(liver_sputum)


coef_ob_sp <- coef(liver_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(liver_sputum)

Liver disease and temperature

liver_temperature <- glm(liver_disease ~ temperature, data = liver_data, family = binomial)


summary(liver_temperature)

coef_ob_temp <- coef(liver_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(liver_temperature)

liver_itchy <- glm(liver_disease ~ itchy_eyes, data = liver_data, family = binomial)

summary(liver_itchy)

liver_chest <- glm(liver_disease ~ chest_pain, data = liver_data, family = binomial)

summary(liver_chest)

liver_joint_p <- glm(liver_disease ~ joint_pain, data = liver_data, family = binomial)

summary(liver_joint_p)

liver_loss_apopetite <- glm(liver_disease ~ loss_appetite, data = liver_data, family = binomial)

summary(liver_loss_apopetite)

Multivariate analysis for liver disease

When adjusting for the variables, in 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, and temperature (38.1-39; 39.1-40) (p ≤ 0.05) for patients with liver disease.
When adjusting for all variables,in patients showing covid-19 symptpms/of patients with positive covid test, in patients with liver disease there was: - 103 % increase in odds of experiencing chills compared to those who do not suffer of liver disease - 13 % increase in loss of smell and taste compared to those who do not suffer of liver disease - 15 % increase in muscle ache compred to those who do not suffer of liver disease - 272 % increase in nausea and vomiting compared to those who do not suffer of liver disease -17 % increase in nasal congestion compared to those who do not suffer of liver disease - 14 % increase in 37.5-38 temperature compared to those who do not suffer of liver disease - 98 % increase in 38.1-39 temperature compared to those who do not suffer of liver disease - 338 % increase ?? in 39.1-41 temperature - 21 % increase in sputum compared to those who do not suffer of liver disease

liver_model <- glm(liver_disease ~ chills + cough + loss_smell_taste + muscle_ache +  nasal_congestion + 
                     temperature + chest_pain + joint_pain + loss_appetite, data = liver_data, family = binomial)

summary(liver_model)

exp(cbind(OR = coef(liver_model), confint(liver_model)))

vif(liver_model)

lung_condition_data <- data_categ_nosev %>%
  dplyr::select(lung_condition, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature,  joint_pain, chest_pain, itchy_eyes, loss_appetite) %>%
  tidyr::drop_na()

lung_count <- lung_condition_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(lung_condition== "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Lung condition across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_lung_sympt <-
  ggplot2::ggplot(lung_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(lung_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_lung_sympt

Univariate analysis for lung condition and Covid-19 symptoms

Univariate logistic regression for lung condition and covid symptoms reveal: - nausea and vomiting, shortness of breath, sputum and 39.1- 41 temperature are statistically significant by looking at p values

Lung condition and chills

lung_condition_chills <- glm(lung_condition ~ chills, data = lung_condition_data, family = binomial)

summary(lung_condition_chills)


coef_lung_condition_chills <- coef(lung_condition_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_lung_condition_chills)
odd_ratios_ob_ch

Lung condition and cough

lung_condition_cough <- glm(lung_condition ~ cough, data = lung_condition_data, family = binomial)

summary(lung_condition_cough)


coef_lung_condition_cough <- coef(lung_condition_cough)

odd_ratios_ob_co <- exp(coef_lung_condition_cough)

odd_ratios_ob_co

Lung condition and diarhoea

lung_condition_diarrhea <- glm(lung_condition ~ diarrhoea, data = lung_condition_data, family = binomial)

summary(lung_condition_diarrhea)


# get coef
coef_ob_diarrhea <- coef(lung_condition_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

Lung condition and headache

lung_condition_headache <- glm(lung_condition ~ headache, data = lung_condition_data, family = binomial)

summary(lung_condition_headache)

coef_ob_head <- coef(lung_condition_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

Lung condition and loss of smell and taste

lung_condition_loss_smell <- glm(lung_condition ~ loss_smell_taste, data = lung_condition_data, family = binomial)


summary(lung_condition_loss_smell)

coef_ob_loss_smell <- coef(lung_condition_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

Lung condition and muscle ache

lung_condition_muscle_ache <- glm(lung_condition ~ muscle_ache, data = lung_condition_data, family = binomial)

summary(lung_condition_muscle_ache)

coef_ob_muscle_ac <- coef(lung_condition_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

Lung condition and nasal congestion

lung_condition_nasal_cong <- glm(lung_condition ~ nasal_congestion, data = lung_condition_data, family = binomial)

summary(lung_condition_nasal_cong)


coef_ob_nas_cong <- coef(lung_condition_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

Lung condition and nausea and vomiting

lung_condition_nausea_vomitting <- glm(lung_condition ~ nausea_vomiting, data = lung_condition_data, family = binomial)

summary(lung_condition_nausea_vomitting)


coef_ob_naus_vom <- coef(lung_condition_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

Lung condition and shorthness of breath

lung_condition_short_breath <- glm(lung_condition ~ shortness_breath, data = lung_condition_data, family = binomial)

summary(lung_condition_short_breath)

coef_ob_sh_br <- coef(lung_condition_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

Lung condition and sore throat

lung_condition_sore_thr <- glm(lung_condition ~ sore_throat, data = lung_condition_data, family = binomial)

summary(lung_condition_sore_thr)

coef_ob_sore_thr <- coef(lung_condition_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

Lung condition and sputum

lung_condition_sputum <- glm(lung_condition ~ sputum, data = lung_condition_data, family = binomial)


summary(lung_condition_sputum)


coef_ob_sp <- coef(lung_condition_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(lung_condition_sputum)

Lung condition and temperature

lung_condition_temperature <- glm(lung_condition ~ temperature, data = lung_condition_data, family = binomial)


summary(lung_condition_temperature)

coef_ob_temp <- coef(lung_condition_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(lung_condition_temperature)

lung_condition_itchy_eyes <- glm(lung_condition ~ itchy_eyes, data = lung_condition_data, family = binomial)

summary(lung_condition_itchy_eyes)

lung_condition_joint_pain <- glm(lung_condition ~ joint_pain, data = lung_condition_data, family = binomial)
summary(lung_condition_joint_pain)

lung_condition_chest_pain <- glm(lung_condition ~ chest_pain, data = lung_condition_data, family = binomial)

summary(lung_condition_chest_pain)

lung_condition_loss_appetite <- glm(lung_condition ~ loss_appetite, data = lung_condition_data, family = binomial)

summary(lung_condition_loss_appetite)

Multivariate analysis for lung condition

Adding all variables that showed an association with the lung diseease.

When adjusting for the above variables, in patients showing covid-19 symptoms/of patients with positivie covid test, there was: - 88 % increase in the odds of experiencing nausea and vomiting compared to those who did not have lung disease; - 63 % increase in odds of experiencing shortness of breath compared to those who did not have lung disease; - 146 % increase in 39.1-41 temperature compared to those who did not have lung disease; - 33 % increase in the odds of experiencing sputum in patients with lung disease compared to those who did not have lung disease

lung_condition_model <- glm(lung_condition ~  chills + cough  + diarrhoea + loss_smell_taste + nausea_vomiting + shortness_breath +
                              sputum + joint_pain + chest_pain , data = lung_condition_data, family = binomial)

summary(lung_condition_model)

exp(cbind(OR = coef(lung_condition_model), confint(lung_condition_model)))


vif(lung_condition_model)

kidney_data <- data_categ_nosev %>%
  dplyr::select(kidney_disease, chills, cough, diarrhoea, headache, loss_smell_taste, muscle_ache, 
                nasal_congestion, nausea_vomiting, shortness_breath, sore_throat, sputum, temperature, chest_pain, joint_pain, loss_appetite, itchy_eyes) %>%
  tidyr::drop_na()

kidney_count <- kidney_data %>%
  tidyr::pivot_longer(cols = 2:17, 
                      names_to = "symptoms", 
                      values_to = "yes_no") %>%
  dplyr::filter(kidney_disease == "Yes" & yes_no == "Yes") %>%
  dplyr::group_by(symptoms) %>%
  dplyr::tally() %>%
  dplyr::mutate(Percentage = n/sum(n)) %>%
  dplyr::arrange(desc(n))

start_date = as.Date("2020-04-09", tz = "Europe/London")
end_date = as.Date("2020-08-18")
title_stub <- "Kidney disease across symptoms\n"
start_date_title <- format(as.Date(start_date), format = "%d %B %Y")
end_date_title <- format(as.Date(end_date), format = "%d %B %Y")
chart_title <- paste0(title_stub, start_date_title, " to ", end_date_title)

plot_kidney_sympt <-
  ggplot2::ggplot(kidney_count, ggplot2::aes(x = reorder(symptoms, - Percentage), y = n, fill = n)) +
  ggplot2::coord_flip() +
  ggplot2::geom_bar(stat = "identity", position = "dodge") +
  ggplot2::scale_fill_viridis_c(option = "magma", direction = -1) +
  ggplot2::scale_x_discrete(limits = unique(kidney_count$symptoms)) +
  #ggplot2::theme(legend.position = "bottom") +
  #ggplot2::guides(fill = ggplot2::guide_legend(nrow = 3)) +
  ggplot2::theme_minimal() +
  ggplot2::labs( title = chart_title,
                 subtitle = "Counts of patients with comorbidities accross symptoms",
                 y = "Counts",
                 x = "Symptoms",
                 caption = "Source: Dataset - Your.md Dataset") +
  ggplot2::theme(
    axis.title.y = ggplot2::element_text(margin = ggplot2::margin(
      t = 0,
      r = 21,
      b = 0,
      l = 0
    )),
    plot.title = ggplot2::element_text(size = 10, face = "bold"),
    plot.subtitle = ggplot2::element_text(size = 9),
    axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
  )

plot_kidney_sympt

Univariate analysis for kidney disease and Covid-19 symptoms

The most Covid symptoms that are associated with kidney disease are shorthness and breath and temperature.

Kidney disease and chills

kidney_chills <- glm(kidney_disease ~ chills, data = kidney_data, family = binomial)

summary(kidney_chills)


coef_kidney_chills <- coef(kidney_chills)

# odd ratios 
odd_ratios_ob_ch <- exp(coef_kidney_chills)
odd_ratios_ob_ch

Kidney disease and cough

kidney_cough <- glm(kidney_disease ~ cough, data = kidney_data, family = binomial)

summary(kidney_cough)


coef_kidney_cough <- coef(kidney_cough)

odd_ratios_ob_co <- exp(coef_kidney_cough)

odd_ratios_ob_co

Kidney disease and diarrhoea

kidney_diarrhea <- glm(kidney_disease ~ diarrhoea, data = kidney_data, family = binomial)

summary(kidney_diarrhea)


# get coef
coef_ob_diarrhea <- coef(kidney_diarrhea)

# odd ratios
odd_ratio_ob_diar <- exp(coef_ob_diarrhea)

odd_ratio_ob_diar

Kidney disease and headache

kidney_headache <- glm(kidney_disease ~ headache, data = kidney_data, family = binomial)

summary(kidney_headache)

coef_ob_head <- coef(kidney_headache)

odd_ratio_ob_head <- exp(coef_ob_head)

odd_ratio_ob_head

Kidney disease and loss of smell and taste

kidney_loss_smell <- glm(kidney_disease ~ loss_smell_taste, data = kidney_data, family = binomial)


summary(kidney_loss_smell)

coef_ob_loss_smell <- coef(kidney_loss_smell)

odd_ratio_ob_los <- exp(coef_ob_loss_smell)

odd_ratio_ob_los

Kidney disease and muscle ache

kidney_muscle_ache <- glm(kidney_disease ~ muscle_ache, data = kidney_data, family = binomial)

summary(kidney_muscle_ache)

coef_ob_muscle_ac <- coef(kidney_muscle_ache)

odd_ratio_ob_los <- exp(coef_ob_muscle_ac)

odd_ratio_ob_los

Kidney disease and nasal congestion

kidney_nasal_cong <- glm(kidney_disease ~ nasal_congestion, data = kidney_data, family = binomial)

summary(kidney_nasal_cong)


coef_ob_nas_cong <- coef(kidney_nasal_cong)

odd_ratio_ob_nas_cong <- exp(coef_ob_nas_cong)

odd_ratio_ob_nas_cong

Kidney disease and nausea and vomiting

kidney_nausea_vomitting <- glm(kidney_disease ~ nausea_vomiting, data = kidney_data, family = binomial)

summary(kidney_nausea_vomitting)


coef_ob_naus_vom <- coef(kidney_nausea_vomitting)

odd_ratio_ob_naus_vom <- exp(coef_ob_naus_vom)

odd_ratio_ob_naus_vom

Kidney disease and shorthness of breath

kidney_short_breath <- glm(kidney_disease ~ shortness_breath, data = kidney_data, family = binomial)

summary(kidney_short_breath)

coef_ob_sh_br <- coef(kidney_short_breath)


odd_ratio_ob_sh_br <- exp(coef_ob_sh_br)

odd_ratio_ob_sh_br

Kidney disease and sore throat

kidney_sore_thr <- glm(kidney_disease ~ sore_throat, data = kidney_data, family = binomial)

summary(kidney_sore_thr)

coef_ob_sore_thr <- coef(kidney_sore_thr)


odd_ratio_ob_sore_thr <- exp(coef_ob_sore_thr)

odd_ratio_ob_sore_thr

Kidney disease and sputum

kidney_sputum <- glm(kidney_disease ~ sputum, data = kidney_data, family = binomial)


summary(kidney_sputum)


coef_ob_sp <- coef(kidney_sputum)

odd_ratio_ob_sp <- exp(coef_ob_sp)

odd_ratio_ob_sp

vif(kidney_sputum)

Kidney disease and temperature

kidney_temperature <- glm(kidney_disease ~ temperature, data = kidney_data, family = binomial)


summary(kidney_temperature)

coef_ob_temp <- coef(kidney_temperature)

odd_ratio_ob_temp <- exp(coef_ob_temp)

odd_ratio_ob_temp

vif(kidney_temperature)

kidney_itchy_eyes <- glm(kidney_disease ~ itchy_eyes, data = kidney_data, family = binomial)

summary(kidney_itchy_eyes)

kidney_joint_pain <- glm(kidney_disease ~ joint_pain, data = kidney_data, family = binomial)

summary(kidney_joint_pain)

kidney_chest_pain <- glm(kidney_disease ~ chest_pain, data = kidney_data, family = binomial)

summary(kidney_chest_pain)

kidney_loss_appetite <- glm(kidney_disease ~ loss_appetite, data = kidney_data, family = binomial)

summary(kidney_loss_appetite)

Multivariate analysis for Kidney disease

The selected variables for the final model are: shortness of breath, temperature.

In patients showing covid-19 symptoms/of patients with a positive covid test,when adjusting for all relevant variables, in respondents with kidney disease there was a: - 64% increase in the odds of experiencing shortness of breaht compared to those who do not have kidney disease - 33 % increase in the odds of experiencing 38.1 -39 temperature compared to those who do not have kidney disease - 305 % ?? not sure - increase in odds of experiencing 39.1-41 temperature compared to those who do not have kidney disease

kidney_model <- glm(kidney_disease ~  muscle_ache + temperature + chest_pain, data = kidney_data, family = binomial)

summary(kidney_model)

exp(cbind(OR = coef(kidney_model), confint(kidney_model)))
vif(kidney_model)

gabrielburcea/cvindia documentation built on Feb. 17, 2021, 3:31 a.m.

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Note that we can't provide technical support on individual packages. You should contact the package authors for that.

gabrielburcea/cvindia
Analysis of symptoms

In gabrielburcea/cvindia: Analysis of symptoms

II. Association analysis.

Correlations

Univariate analysis

Univariate analysis for asthma

Multivariable Logistic Regression for Asthma

Univariate analysis for diabetes type one

Multivariate analysis for diabetest type one

Univariate analysis for diabetes type one

Multivariable analysis for diabetes type two

Univariate analysis

Multivariate analysis for heart disease

Univariate analysis for hypertension and Covid symptoms

Multivariable analysis for hypertension

Univariate analysis for liver disease and Covid-19 symptoms

Multivariate analysis for liver disease

Univariate analysis for lung condition and Covid-19 symptoms

Multivariate analysis for lung condition

Univariate analysis for kidney disease and Covid-19 symptoms

Multivariate analysis for Kidney disease

R Package Documentation

Browse R Packages

We want your feedback!

gabrielburcea/cvindia Analysis of symptoms

In gabrielburcea/cvindia: Analysis of symptoms

II. Association analysis.

Correlations

Univariate analysis

Univariate analysis for asthma

Multivariable Logistic Regression for Asthma

Univariate analysis for diabetes type one

Multivariate analysis for diabetest type one

Univariate analysis for diabetes type one

Multivariable analysis for diabetes type two

Univariate analysis

Multivariate analysis for heart disease

Univariate analysis for hypertension and Covid symptoms

Multivariable analysis for hypertension

Univariate analysis for liver disease and Covid-19 symptoms

Multivariate analysis for liver disease

Univariate analysis for lung condition and Covid-19 symptoms

Multivariate analysis for lung condition

Univariate analysis for kidney disease and Covid-19 symptoms

Multivariate analysis for Kidney disease

R Package Documentation

Browse R Packages

We want your feedback!

gabrielburcea/cvindia
Analysis of symptoms