R/cleaning_scripts/Run_this_first.R
In gabrielburcea/cvindia: Analysis of symptoms
# library(tidyverse)
# data <- PivotMappe060520r
# data_select <- data %>%
# dplyr::select(ID, Age, Gender, Location, Country, Chills, Cough, Diarrhoea, Fatigue, Headcahe, 'Healthcare Worker', 'How Unwell',
# 'Long Standing Health Issues', 'Loss of smell and taste', 'Muscle Ache', 'Nasal Congestion', 'Nausea and Vomiting', 'Number Of Days Symptoms Showing',
# 'Pregnant', 'Self Diagnosis', 'Shortness of Breath', 'Sore Throat','Reason For Helping', 'Sputum', 'Temperature') %>%
# dplyr::rename( id = ID,
# age = Age,
# gender = Gender,
# location = Location,
# country = Country,
# chills = Chills,
# diarrhoea = Diarrhoea,
# fatigue = Fatigue,
# headache = Headcahe,
# healthcare_worker = 'Healthcare Worker',
# how_unwell = 'How Unwell',
# long_standing_health = 'Long Standing Health Issues',
# loss_smell_taste = 'Loss of smell and taste',
# muscle_ache = 'Muscle Ache',
# nasal_congestion = 'Nasal Congestion',
# nausea_vomiting = 'Nausea and Vomiting',
# no_days_symptoms_show = 'Number Of Days Symptoms Showing',
# pregnant = 'Pregnant',
# shortness_breath = 'Shortness of Breath',
# sore_throat = 'Sore Throat',
# sputum = 'Sputum',
# temperature = 'Temperature',
# self_diagnosis = 'Self Diagnosis',
# tested_or_not = 'Reason For Helping')
#
# data_select$tested_or_not <- as.factor(data_select)
#
# test_data <- data_select %>%
# tidyr::separate('long_standing_health', c('comorbidity_one', 'comorbidity_two', 'comorbidity_three', 'comorbidity_four'), sep = ",") %>%
# tidyr::replace_na(list('comorbidity_one' = 'None', 'comorbidity_two' = 'None', 'comorbidity_three' = 'None', 'comorbidity_four' = 'None'))
#
# test_data[test_data == 0] <- NA
#
# data_rec <- test_data %>%
# dplyr::mutate(tested_covid = stringr::str_match(tested_or_not, 'Positive')) %>%
# dplyr::mutate(tested_covid = stringr::str_match(tested_or_not, 'Positive')) %>%
# tidyr::replace_na(list('tested_covid' = 'Negative')) %>%
# tidyr::replace_na(list('no_days_symptoms_show' = 'None' )) %>%
# dplyr::select(id, age, gender, country, chills, Cough, diarrhoea, fatigue, healthcare_worker,
# how_unwell, comorbidity_one, loss_smell_taste, muscle_ache, nasal_congestion, nausea_vomiting,
# no_days_symptoms_show, self_diagnosis, shortness_breath, sore_throat, sputum, temperature, tested_covid)
#
# write.csv(data_rec, file = "/Users/gabrielburcea/Rprojects/data/data_rec.csv")
# count_positive_negative <- test_data %>%
# dplyr::select(id, tested_covid) %>%
# dplyr::group_by(tested_covid) %>%
# tally()
# asthma <- test_data %>%
# dplyr::filter(comorbidity_one == 'Asthma (managed with an inhaler)' | comorbidity_one == "None")
#
#
# long_standing_lung_condition <- test_data %>%
# dplyr::filter(comorbidity_one == 'Long-Standing Lung Condition' | comorbidity_one == 'None')
#
# high_blood_pressure <- test_data %>%
# dplyr::filter(comorbidity_one == 'High Blood Pressure (hypertension)' | comorbidity_one == "None")
#
# obesity <- test_data %>%
# dplyr::filter(comorbidity_one == 'Obesity' | comorbidity_one == "None")
# dt_select <- dt_select %>%
# dplyr::mutate(Age_band = if_else(age == 0 , '0',
# age == 1 | age <= 4 ~ '1-4',
# age == 5 | age <= 9 ~ '5-9',
# age == 10 | age <= 14 ~ '10-14',
# age == 15 | age <= 19 ~ '15-19',
# age == 20 | age <= 24 ~ '20-24',
# age == 25 | age <= 29 ~ '25-29',
# age == 30 | age <= 34 ~ '30-34',
# age == 35 | age <= 39 ~ '35-39',
# age == 40 | age <= 44 ~ '40-44',
# age == 45 | age <= 49 ~ '45-49',
# age == 50 | age <= 54 ~ '50-54',
# age == 55 | age <= 59 ~ '55-59',
# age == 60 | age <= 64 ~ '60-64',
# age == 65 | age <= 69 ~ '65-69',
# age == 70 | age <= 74 ~ '70-74',
# age == 75 | age <= 79 ~ '75-79',
# age == 80 | age <= 84 ~ '80-84',
# age == 85 | age <= 89 ~ '85-89',
# age == 90 | age <= 94 ~ '90-94',
# age >= 95 ~ '95+'))
# data_rec <- read.csv("/Users/gabrielburcea/Rprojects/data/PivotMappe060520r.csv", header = TRUE, sep = ",")
# data_select <- data_rec %>%
# #### 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 = 'Yes') %>%
# tidyr::pivot_wider(id_cols = -c(Comorbidity, Condition), names_from = Comorbidity, values_from = Condition, values_fill = list(Condition = 'No')) %>%
# dplyr::select(-None)
########################################
#### 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)
# level_key <-
# c(
# "None" = 'none',
# "Curious" = "none",
# 'Showing Symptoms But Not Tested,Curious' = "showing symptoms",
# 'Showing Symptoms But Not Tested' = "showing symptoms",
# 'Self-Isolating With No Symptoms' = "none",
# 'Showing Symptoms But Not Tested,Curious,Self-Isolating With No Symptoms' = "showing symptoms",
# 'Tested Positive' = 'positive',
# 'Curious,Self-Isolating With No Symptoms' = 'none',
# 'Tested Negative But Have Symptoms' = 'showing symptoms',
# 'Recovered But Have New Symptoms' = 'positive',
# 'Live With Someone With Coronavirus' = 'live_with_scorona',
# 'Live With Someone With Coronavirus,Curious' = 'live_with_scorona',
# 'Tested Negative But Have Symptoms,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Tested Negative But Have Symptoms,Curious' = 'showing symptoms',
# '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' = 'showing symptoms',
# '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' = 'showing symptoms',
# 'Showing Symptoms But Not Tested,Recovered But Have New Symptoms' = 'showing symptoms',
# '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' = 'positive',
# 'Live With Someone With Coronavirus,Self-Isolating With No Symptoms' = 'live_with_scorona',
# 'Tested Positive,Recovered But Have New Symptoms' = 'positive',
# 'Live With Someone With Coronavirus,Curious,Self-Isolating With No Symptoms' = 'live_with_scorona',
# 'Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious' = 'showing symptoms',
# 'Recovered But Have New Symptoms,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Tested Positive,Tested Negative But Have Symptoms,Recovered But Have New Symptoms' = 'showing symptoms',
# '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' = 'showing symptoms',
# 'Showing Symptoms But Not Tested,Live With Someone With Coronavirus' = 'showing symptoms',
# 'Tested Positive,Recovered But Have New Symptoms,Curious' = 'positive',
# 'Tested Negative But Have Symptoms,Curious,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Curious' = 'showing symptoms'
# )
# #################################################
# ######### Get a numeric dataset #################
# #################################################
# level_key_temperature <-
# c( "38.1-39" = '38.2-39',
# "38.1-39" = 'Temperature')
# level_no_days_sympt_show <-
# c('21' = "More than 21")
#
# data_model <- data_rec %>%
# dplyr::mutate(Covid_tested = dplyr::recode(tested_or_not, !!!level_key),
# number_days_symptoms = forcats::fct_recode(Number.Of.Days.Symptoms.Showing, !!!level_no_days_sympt_show) )
# data_model$gender <- as.factor(data_model$Gender)
# data_model$country <- as.factor(data_model$Country)
# data_model$chills <- as.factor(data_model$Chills)
# data_model$cough <- as.factor(data_model$Cough)
# data_model$diarrhoea <- as.factor(data_model$Diarrhoea)
# data_model$fatigue <- as.factor(data_model$Fatigue)
# data_model$headache <- as.factor(data_model$Headcahe)
# data_model$loss_smell_taste <- as.factor(data_model$Loss.of.smell.and.taste)
# data_model$muscle_ache <- as.factor(data_model$Muscle.Ache)
# data_model$nasal_congestion <- as.factor(data_model$Nasal.Congestion)
# data_model$nausea_vomiting <- as.factor(data_model$Nausea.and.Vomiting)
# data_model$self_diagnosis <- as.factor(data_model$Self.Diagnosis)
# data_model$shortness_breath <- as.factor(data_model$Shortness.of.Breath)
# data_model$sore_throat <- as.factor(data_model$Sore.Throat)
# data_model$sputum <- as.factor(data_model$Sputum)
# data_model$temperature <- as.factor(data_model$Temperature)
# data_model$health_care_worker <- as.factor(data_model$Healthcare.Worker)
# data_model$care_home_worker <- as.factor(data_model$Care.Home.Worker)
# data_model$asthma <- as.factor(data_model$`Asthma (managed with an inhaler)`)
# data_model$diabetes_type_two <- as.factor(data_model$`Diabetes Type 2`)
# data_model$obesity <- as.factor(data_model$Obesity)
# data_model$hypertension <- as.factor(data_model$`High Blood Pressure (hypertension)`)
# data_model$heart_disease <- as.factor(data_model$`Long-Standing Heart Disease`)
# data_model$kidney_disease <- as.factor(data_model$`Long-Standing Kidney Disease`)
# data_model$lung_condition <- as.factor(data_model$`Long-Standing Lung Condition`)
# data_model$liver_disease <- as.factor(data_model$`Long-Standing Liver Disease`)
# data_model$diabetes_type_one <- as.factor(data_model$`Diabetes Type 1 (controlled by insulin)`)
# data_model$how_unwell <- as.factor(data_model$How.Unwell)
# data_model$age <- as.factor(data_model$Age)
# data_model$covid_tested <- as.factor(data_model$Covid_tested)
# data_selected$number_days_symptoms <- as.numeric(data_selected$number_days_symptoms)
# #### Refactor the levels ##################################################
# data_sel<- data_model %>%
# dplyr::rename(location = Location, date_completed = Date.Completed, pregnant = Pregnant, id = ID) %>%
# dplyr::select(id,
# covid_tested,
# tested_or_not,
# age,
# gender,
# country,
# location,
# date_completed,
# care_home_worker,
# health_care_worker,
# how_unwell,
# self_diagnosis,
# chills,
# cough,
# diarrhoea,
# fatigue,
# headache,
# how_unwell,
# loss_smell_taste,
# muscle_ache,
# nasal_congestion,
# nausea_vomiting,
# number_days_symptoms,
# pregnant,
# self_diagnosis,
# shortness_breath,
# sore_throat,
# sputum,
# temperature,
# asthma,
# diabetes_type_one,
# diabetes_type_two,
# obesity,
# hypertension,
# heart_disease,
# lung_condition,
# liver_disease,
# hypertension,
# kidney_disease)
#
# write.csv(data_sel, file = "/Users/gabrielburcea/Rprojects/data/data_descr_15062020.csv", row.names = FALSE)
# level_key_chills <-
# c( 'Yes' = "Chills",
# 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_cough <-
# c( 'Yes' = "Cough",
# 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_diarrhoea <-
# c( 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_fatigue <-
# c( 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_headache <-
# c('No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe",
# 'Yes' = "Headcahe")
# level_key_loss_smell_taste <-
# c( 'Yes' = "Loss of smell and taste",
# 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_muschle_ache <-
# c( 'No' = "No",
# 'Yes' = "Muscle Ache",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_nasal_congestion <-
# c( 'No' = "No",
# 'Yes' = "Nasal Congestion",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_nausea_vomiting <-
# c( 'No' = "No",
# 'Yes' = "Nausea and Vomiting",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_self_diagnosis <-
# c( 'No' = "None",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_short_breath <-
# c( 'No' = "No",
# 'Yes' = "Shortness of Breath",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_sore_throat <-
# c( 'No' = "No",
# 'Yes' = "Sore Throat",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_sputum <-
# c( 'No' = "No",
# 'Yes' = "Sputum",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_care_home_worker <-
# c('Yes' = 'Yes',
# 'No' = 'No')
#### Refactor the levels ##################################################
# data_not_sev <- data_sel %>%
# dplyr::mutate(chills = forcats::fct_recode(chills, !!!level_key_chills),
# cough = forcats::fct_recode(cough, !!!level_key_cough),
# diarrhoea = forcats::fct_recode(diarrhoea, !!!level_key_diarrhoea),
# fatigue = forcats::fct_recode(fatigue, !!!level_key_fatigue),
# headache = forcats::fct_recode(headache, !!!level_key_headache),
# loss_smell_taste = forcats::fct_recode(loss_smell_taste, !!!level_key_loss_smell_taste),
# muscle_ache = forcats::fct_recode(muscle_ache, !!!level_key_muschle_ache),
# nasal_congestion = forcats::fct_recode(nasal_congestion, !!!level_key_nasal_congestion),
# nausea_vomiting = forcats::fct_recode(nausea_vomiting, !!!level_key_nausea_vomiting),
# self_diagnosis = forcats::fct_recode(self_diagnosis, !!!level_key_self_diagnosis),
# shortness_breath = forcats::fct_recode(shortness_breath, !!!level_key_short_breath),
# sore_throat = forcats::fct_recode(sore_throat, !!!level_key_sore_throat),
# sputum = forcats::fct_recode(sputum, !!!level_key_sputum),
# temperature = forcats::fct_recode(temperature, !!!level_key_temperature),
# care_home_worker = forcats::fct_recode(care_home_worker, !!!level_key_care_home_worker))
#
#
#write.csv(data_not_sev, file = "/Users/gabrielburcea/Rprojects/data/data_no_sev.csv", row.names = FALSE)
#
# test <- data_categ_nosev %>%
# dplyr::mutate(asthma_diabetes_one = if_else(asthma == 'Yes' | diabetes_type_one == "Yes" , TRUE, FALSE),
# asthma_diabetes_two = if_else(asthma == 'Yes' | diabetes_type_two == "Yes" , TRUE, FALSE),
# asthma_hypertension = if_else(asthma == 'Yes' | hypertension == 'Yes' , TRUE, FALSE),
# asthma_obesity = if_else(asthma == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# asthma_heart_disease = if_else(asthma == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# asthma_lung_cond = if_else(asthma == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# asthma_liver_disease = if_else(asthma == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# asthma_kidney_disease = if_else(asthma == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# diabetes_one_diabetes_two = if_else(diabetes_type_one == 'Yes' | diabetes_type_one == "Yes" , TRUE,FALSE ),
# diabetes_one_hypertension = if_else(diabetes_type_one == 'Yes' | hypertension == 'Yes' , TRUE, FALSE),
# diabetes_one_obesity = if_else(diabetes_type_one == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# diabetes_one_heart_disease = if_else(diabetes_type_one == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# diabetes_one_lung_cond = if_else(diabetes_type_one == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE ),
# diabetes_one_liver_disease = if_else(diabetes_type_one == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# diabetes_one_kidney_disease = if_else(diabetes_type_one == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
#
# diabetes_two_hypertension = if_else(diabetes_type_two == 'Yes' | hypertension == 'Yes' , TRUE, FALSE),
# diabetes_two_obesity = if_else(diabetes_type_two == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# diabetes_two_disease = if_else(diabetes_type_two == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# diabetes_two_lung_cond = if_else(diabetes_type_two == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# diabetes_two_liver_disease = if_else(diabetes_type_two == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# diabetes_two_kidney_disease = if_else(diabetes_type_two == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# hypertension_obesity = if_else(hypertension == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# hypertension_heart_disease = if_else(hypertension == 'Yes' | heart_disease == 'Yes' , TRUE,FALSE ),
# hypertension_lung_cond = if_else(hypertension == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# hypertension_liver_disease = if_else(hypertension == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# hypertension_kidney_disease = if_else(hypertension == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# obesity_heart_disease = if_else(obesity == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# obesity_lung_cond = if_else(obesity == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# obesity_liver_disease = if_else(obesity == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# obesity_kidney_disease = if_else(obesity == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# heart_disease_lung_cond = if_else(heart_disease == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE ),
# heart_disease_liver_disease = if_else(heart_disease == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# heart_disease_kidney_disease = if_else(heart_disease == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# lung_condition_liver_disease = if_else(lung_condition == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# lung_condition_kidney_disease = if_else(lung_condition == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# liver_disease_kidney_disease = if_else(liver_disease == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE))
#
#
# write.csv(test, file = "/Users/gabrielburcea/Rprojects/data/data_no_sev_stats.csv", row.names = FALSE)
gabrielburcea/cvindia documentation built on Feb. 17, 2021, 3:31 a.m.
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# library(tidyverse)
# data <- PivotMappe060520r
# data_select <- data %>%
# dplyr::select(ID, Age, Gender, Location, Country, Chills, Cough, Diarrhoea, Fatigue, Headcahe, 'Healthcare Worker', 'How Unwell',
# 'Long Standing Health Issues', 'Loss of smell and taste', 'Muscle Ache', 'Nasal Congestion', 'Nausea and Vomiting', 'Number Of Days Symptoms Showing',
# 'Pregnant', 'Self Diagnosis', 'Shortness of Breath', 'Sore Throat','Reason For Helping', 'Sputum', 'Temperature') %>%
# dplyr::rename( id = ID,
# age = Age,
# gender = Gender,
# location = Location,
# country = Country,
# chills = Chills,
# diarrhoea = Diarrhoea,
# fatigue = Fatigue,
# headache = Headcahe,
# healthcare_worker = 'Healthcare Worker',
# how_unwell = 'How Unwell',
# long_standing_health = 'Long Standing Health Issues',
# loss_smell_taste = 'Loss of smell and taste',
# muscle_ache = 'Muscle Ache',
# nasal_congestion = 'Nasal Congestion',
# nausea_vomiting = 'Nausea and Vomiting',
# no_days_symptoms_show = 'Number Of Days Symptoms Showing',
# pregnant = 'Pregnant',
# shortness_breath = 'Shortness of Breath',
# sore_throat = 'Sore Throat',
# sputum = 'Sputum',
# temperature = 'Temperature',
# self_diagnosis = 'Self Diagnosis',
# tested_or_not = 'Reason For Helping')
#
# data_select$tested_or_not <- as.factor(data_select)
#
# test_data <- data_select %>%
# tidyr::separate('long_standing_health', c('comorbidity_one', 'comorbidity_two', 'comorbidity_three', 'comorbidity_four'), sep = ",") %>%
# tidyr::replace_na(list('comorbidity_one' = 'None', 'comorbidity_two' = 'None', 'comorbidity_three' = 'None', 'comorbidity_four' = 'None'))
#
# test_data[test_data == 0] <- NA
#
# data_rec <- test_data %>%
# dplyr::mutate(tested_covid = stringr::str_match(tested_or_not, 'Positive')) %>%
# dplyr::mutate(tested_covid = stringr::str_match(tested_or_not, 'Positive')) %>%
# tidyr::replace_na(list('tested_covid' = 'Negative')) %>%
# tidyr::replace_na(list('no_days_symptoms_show' = 'None' )) %>%
# dplyr::select(id, age, gender, country, chills, Cough, diarrhoea, fatigue, healthcare_worker,
# how_unwell, comorbidity_one, loss_smell_taste, muscle_ache, nasal_congestion, nausea_vomiting,
# no_days_symptoms_show, self_diagnosis, shortness_breath, sore_throat, sputum, temperature, tested_covid)
#
# write.csv(data_rec, file = "/Users/gabrielburcea/Rprojects/data/data_rec.csv")
# count_positive_negative <- test_data %>%
# dplyr::select(id, tested_covid) %>%
# dplyr::group_by(tested_covid) %>%
# tally()
# asthma <- test_data %>%
# dplyr::filter(comorbidity_one == 'Asthma (managed with an inhaler)' | comorbidity_one == "None")
#
#
# long_standing_lung_condition <- test_data %>%
# dplyr::filter(comorbidity_one == 'Long-Standing Lung Condition' | comorbidity_one == 'None')
#
# high_blood_pressure <- test_data %>%
# dplyr::filter(comorbidity_one == 'High Blood Pressure (hypertension)' | comorbidity_one == "None")
#
# obesity <- test_data %>%
# dplyr::filter(comorbidity_one == 'Obesity' | comorbidity_one == "None")
# dt_select <- dt_select %>%
# dplyr::mutate(Age_band = if_else(age == 0 , '0',
# age == 1 | age <= 4 ~ '1-4',
# age == 5 | age <= 9 ~ '5-9',
# age == 10 | age <= 14 ~ '10-14',
# age == 15 | age <= 19 ~ '15-19',
# age == 20 | age <= 24 ~ '20-24',
# age == 25 | age <= 29 ~ '25-29',
# age == 30 | age <= 34 ~ '30-34',
# age == 35 | age <= 39 ~ '35-39',
# age == 40 | age <= 44 ~ '40-44',
# age == 45 | age <= 49 ~ '45-49',
# age == 50 | age <= 54 ~ '50-54',
# age == 55 | age <= 59 ~ '55-59',
# age == 60 | age <= 64 ~ '60-64',
# age == 65 | age <= 69 ~ '65-69',
# age == 70 | age <= 74 ~ '70-74',
# age == 75 | age <= 79 ~ '75-79',
# age == 80 | age <= 84 ~ '80-84',
# age == 85 | age <= 89 ~ '85-89',
# age == 90 | age <= 94 ~ '90-94',
# age >= 95 ~ '95+'))
# data_rec <- read.csv("/Users/gabrielburcea/Rprojects/data/PivotMappe060520r.csv", header = TRUE, sep = ",")
# data_select <- data_rec %>%
# #### 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 = 'Yes') %>%
# tidyr::pivot_wider(id_cols = -c(Comorbidity, Condition), names_from = Comorbidity, values_from = Condition, values_fill = list(Condition = 'No')) %>%
# dplyr::select(-None)
########################################
#### 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)
# level_key <-
# c(
# "None" = 'none',
# "Curious" = "none",
# 'Showing Symptoms But Not Tested,Curious' = "showing symptoms",
# 'Showing Symptoms But Not Tested' = "showing symptoms",
# 'Self-Isolating With No Symptoms' = "none",
# 'Showing Symptoms But Not Tested,Curious,Self-Isolating With No Symptoms' = "showing symptoms",
# 'Tested Positive' = 'positive',
# 'Curious,Self-Isolating With No Symptoms' = 'none',
# 'Tested Negative But Have Symptoms' = 'showing symptoms',
# 'Recovered But Have New Symptoms' = 'positive',
# 'Live With Someone With Coronavirus' = 'live_with_scorona',
# 'Live With Someone With Coronavirus,Curious' = 'live_with_scorona',
# 'Tested Negative But Have Symptoms,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Tested Negative But Have Symptoms,Curious' = 'showing symptoms',
# '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' = 'showing symptoms',
# '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' = 'showing symptoms',
# 'Showing Symptoms But Not Tested,Recovered But Have New Symptoms' = 'showing symptoms',
# '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' = 'positive',
# 'Live With Someone With Coronavirus,Self-Isolating With No Symptoms' = 'live_with_scorona',
# 'Tested Positive,Recovered But Have New Symptoms' = 'positive',
# 'Live With Someone With Coronavirus,Curious,Self-Isolating With No Symptoms' = 'live_with_scorona',
# 'Showing Symptoms But Not Tested,Recovered But Have New Symptoms,Curious' = 'showing symptoms',
# 'Recovered But Have New Symptoms,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Recovered But Have New Symptoms,Curious,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Tested Positive,Tested Negative But Have Symptoms,Recovered But Have New Symptoms' = 'showing symptoms',
# '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' = 'showing symptoms',
# 'Showing Symptoms But Not Tested,Live With Someone With Coronavirus' = 'showing symptoms',
# 'Tested Positive,Recovered But Have New Symptoms,Curious' = 'positive',
# 'Tested Negative But Have Symptoms,Curious,Self-Isolating With No Symptoms' = 'showing symptoms',
# 'Tested Negative But Have Symptoms,Showing Symptoms But Not Tested,Curious' = 'showing symptoms'
# )
# #################################################
# ######### Get a numeric dataset #################
# #################################################
# level_key_temperature <-
# c( "38.1-39" = '38.2-39',
# "38.1-39" = 'Temperature')
# level_no_days_sympt_show <-
# c('21' = "More than 21")
#
# data_model <- data_rec %>%
# dplyr::mutate(Covid_tested = dplyr::recode(tested_or_not, !!!level_key),
# number_days_symptoms = forcats::fct_recode(Number.Of.Days.Symptoms.Showing, !!!level_no_days_sympt_show) )
# data_model$gender <- as.factor(data_model$Gender)
# data_model$country <- as.factor(data_model$Country)
# data_model$chills <- as.factor(data_model$Chills)
# data_model$cough <- as.factor(data_model$Cough)
# data_model$diarrhoea <- as.factor(data_model$Diarrhoea)
# data_model$fatigue <- as.factor(data_model$Fatigue)
# data_model$headache <- as.factor(data_model$Headcahe)
# data_model$loss_smell_taste <- as.factor(data_model$Loss.of.smell.and.taste)
# data_model$muscle_ache <- as.factor(data_model$Muscle.Ache)
# data_model$nasal_congestion <- as.factor(data_model$Nasal.Congestion)
# data_model$nausea_vomiting <- as.factor(data_model$Nausea.and.Vomiting)
# data_model$self_diagnosis <- as.factor(data_model$Self.Diagnosis)
# data_model$shortness_breath <- as.factor(data_model$Shortness.of.Breath)
# data_model$sore_throat <- as.factor(data_model$Sore.Throat)
# data_model$sputum <- as.factor(data_model$Sputum)
# data_model$temperature <- as.factor(data_model$Temperature)
# data_model$health_care_worker <- as.factor(data_model$Healthcare.Worker)
# data_model$care_home_worker <- as.factor(data_model$Care.Home.Worker)
# data_model$asthma <- as.factor(data_model$`Asthma (managed with an inhaler)`)
# data_model$diabetes_type_two <- as.factor(data_model$`Diabetes Type 2`)
# data_model$obesity <- as.factor(data_model$Obesity)
# data_model$hypertension <- as.factor(data_model$`High Blood Pressure (hypertension)`)
# data_model$heart_disease <- as.factor(data_model$`Long-Standing Heart Disease`)
# data_model$kidney_disease <- as.factor(data_model$`Long-Standing Kidney Disease`)
# data_model$lung_condition <- as.factor(data_model$`Long-Standing Lung Condition`)
# data_model$liver_disease <- as.factor(data_model$`Long-Standing Liver Disease`)
# data_model$diabetes_type_one <- as.factor(data_model$`Diabetes Type 1 (controlled by insulin)`)
# data_model$how_unwell <- as.factor(data_model$How.Unwell)
# data_model$age <- as.factor(data_model$Age)
# data_model$covid_tested <- as.factor(data_model$Covid_tested)
# data_selected$number_days_symptoms <- as.numeric(data_selected$number_days_symptoms)
# #### Refactor the levels ##################################################
# data_sel<- data_model %>%
# dplyr::rename(location = Location, date_completed = Date.Completed, pregnant = Pregnant, id = ID) %>%
# dplyr::select(id,
# covid_tested,
# tested_or_not,
# age,
# gender,
# country,
# location,
# date_completed,
# care_home_worker,
# health_care_worker,
# how_unwell,
# self_diagnosis,
# chills,
# cough,
# diarrhoea,
# fatigue,
# headache,
# how_unwell,
# loss_smell_taste,
# muscle_ache,
# nasal_congestion,
# nausea_vomiting,
# number_days_symptoms,
# pregnant,
# self_diagnosis,
# shortness_breath,
# sore_throat,
# sputum,
# temperature,
# asthma,
# diabetes_type_one,
# diabetes_type_two,
# obesity,
# hypertension,
# heart_disease,
# lung_condition,
# liver_disease,
# hypertension,
# kidney_disease)
#
# write.csv(data_sel, file = "/Users/gabrielburcea/Rprojects/data/data_descr_15062020.csv", row.names = FALSE)
# level_key_chills <-
# c( 'Yes' = "Chills",
# 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_cough <-
# c( 'Yes' = "Cough",
# 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_diarrhoea <-
# c( 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_fatigue <-
# c( 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_headache <-
# c('No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe",
# 'Yes' = "Headcahe")
# level_key_loss_smell_taste <-
# c( 'Yes' = "Loss of smell and taste",
# 'No' = "No",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_muschle_ache <-
# c( 'No' = "No",
# 'Yes' = "Muscle Ache",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_nasal_congestion <-
# c( 'No' = "No",
# 'Yes' = "Nasal Congestion",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_nausea_vomiting <-
# c( 'No' = "No",
# 'Yes' = "Nausea and Vomiting",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_self_diagnosis <-
# c( 'No' = "None",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_short_breath <-
# c( 'No' = "No",
# 'Yes' = "Shortness of Breath",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_sore_throat <-
# c( 'No' = "No",
# 'Yes' = "Sore Throat",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_sputum <-
# c( 'No' = "No",
# 'Yes' = "Sputum",
# 'Yes' = "Mild",
# 'Yes' = "Moderate",
# 'Yes' = "Severe")
# level_key_care_home_worker <-
# c('Yes' = 'Yes',
# 'No' = 'No')
#### Refactor the levels ##################################################
# data_not_sev <- data_sel %>%
# dplyr::mutate(chills = forcats::fct_recode(chills, !!!level_key_chills),
# cough = forcats::fct_recode(cough, !!!level_key_cough),
# diarrhoea = forcats::fct_recode(diarrhoea, !!!level_key_diarrhoea),
# fatigue = forcats::fct_recode(fatigue, !!!level_key_fatigue),
# headache = forcats::fct_recode(headache, !!!level_key_headache),
# loss_smell_taste = forcats::fct_recode(loss_smell_taste, !!!level_key_loss_smell_taste),
# muscle_ache = forcats::fct_recode(muscle_ache, !!!level_key_muschle_ache),
# nasal_congestion = forcats::fct_recode(nasal_congestion, !!!level_key_nasal_congestion),
# nausea_vomiting = forcats::fct_recode(nausea_vomiting, !!!level_key_nausea_vomiting),
# self_diagnosis = forcats::fct_recode(self_diagnosis, !!!level_key_self_diagnosis),
# shortness_breath = forcats::fct_recode(shortness_breath, !!!level_key_short_breath),
# sore_throat = forcats::fct_recode(sore_throat, !!!level_key_sore_throat),
# sputum = forcats::fct_recode(sputum, !!!level_key_sputum),
# temperature = forcats::fct_recode(temperature, !!!level_key_temperature),
# care_home_worker = forcats::fct_recode(care_home_worker, !!!level_key_care_home_worker))
#
#
#write.csv(data_not_sev, file = "/Users/gabrielburcea/Rprojects/data/data_no_sev.csv", row.names = FALSE)
#
# test <- data_categ_nosev %>%
# dplyr::mutate(asthma_diabetes_one = if_else(asthma == 'Yes' | diabetes_type_one == "Yes" , TRUE, FALSE),
# asthma_diabetes_two = if_else(asthma == 'Yes' | diabetes_type_two == "Yes" , TRUE, FALSE),
# asthma_hypertension = if_else(asthma == 'Yes' | hypertension == 'Yes' , TRUE, FALSE),
# asthma_obesity = if_else(asthma == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# asthma_heart_disease = if_else(asthma == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# asthma_lung_cond = if_else(asthma == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# asthma_liver_disease = if_else(asthma == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# asthma_kidney_disease = if_else(asthma == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# diabetes_one_diabetes_two = if_else(diabetes_type_one == 'Yes' | diabetes_type_one == "Yes" , TRUE,FALSE ),
# diabetes_one_hypertension = if_else(diabetes_type_one == 'Yes' | hypertension == 'Yes' , TRUE, FALSE),
# diabetes_one_obesity = if_else(diabetes_type_one == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# diabetes_one_heart_disease = if_else(diabetes_type_one == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# diabetes_one_lung_cond = if_else(diabetes_type_one == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE ),
# diabetes_one_liver_disease = if_else(diabetes_type_one == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# diabetes_one_kidney_disease = if_else(diabetes_type_one == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
#
# diabetes_two_hypertension = if_else(diabetes_type_two == 'Yes' | hypertension == 'Yes' , TRUE, FALSE),
# diabetes_two_obesity = if_else(diabetes_type_two == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# diabetes_two_disease = if_else(diabetes_type_two == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# diabetes_two_lung_cond = if_else(diabetes_type_two == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# diabetes_two_liver_disease = if_else(diabetes_type_two == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# diabetes_two_kidney_disease = if_else(diabetes_type_two == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# hypertension_obesity = if_else(hypertension == 'Yes' | obesity == 'Yes' , TRUE, FALSE),
# hypertension_heart_disease = if_else(hypertension == 'Yes' | heart_disease == 'Yes' , TRUE,FALSE ),
# hypertension_lung_cond = if_else(hypertension == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# hypertension_liver_disease = if_else(hypertension == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# hypertension_kidney_disease = if_else(hypertension == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# obesity_heart_disease = if_else(obesity == 'Yes' | heart_disease == 'Yes' , TRUE, FALSE),
# obesity_lung_cond = if_else(obesity == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE),
# obesity_liver_disease = if_else(obesity == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# obesity_kidney_disease = if_else(obesity == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# heart_disease_lung_cond = if_else(heart_disease == 'Yes' | lung_condition == 'Yes' , TRUE, FALSE ),
# heart_disease_liver_disease = if_else(heart_disease == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# heart_disease_kidney_disease = if_else(heart_disease == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# lung_condition_liver_disease = if_else(lung_condition == 'Yes' | liver_disease == 'Yes' , TRUE, FALSE),
# lung_condition_kidney_disease = if_else(lung_condition == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE),
#
# liver_disease_kidney_disease = if_else(liver_disease == 'Yes' | kidney_disease == 'Yes' , TRUE, FALSE))
#
#
# write.csv(test, file = "/Users/gabrielburcea/Rprojects/data/data_no_sev_stats.csv", row.names = FALSE)
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