#Import covid CSV
#Create covidData Dataframe
covidData<-read.csv("covid.csv",header=TRUE,stringsAsFactors = FALSE)

#Set NULL Values to 0 for ease of data handling
covidData$new_deaths[is.na(covidData$new_deaths)]<-0

#Create a month colum without date
covidData$Months<-substr(covidData$date,4,10)

#Create location vector for us in summary data frame
location<-c("United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom",
            "United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom","United Kingdom",
            "United Kingdom","United Kingdom",
            "China","China","China","China","China","China","China","China","China","China",
            "China","China","China","China","China","China","China","China","China","China",
            "China","China")

#Create Month vector for use in summary data frame
months<-c(unique(substr(covidData$date,4,10)),unique(substr(covidData$date,4,10)))

#Create a vector full of 0 values for use in data frame
cases<-c(1:44)
for (i in cases)
{cases[i]<-0}

#Create a vector full of 0 values for use in data frame
deaths<-c(1:44)
for (i in deaths)
{deaths[i]<-0}

#Create summary data frame to store barplot values
summary<-data.frame(location=location,months=months,cases=cases,deaths=deaths,stringsAsFactors = FALSE)

#loop through values and assign to summary data frame
for (i in seq(1:length(covidData$new_cases)))
{
if (covidData[i,3]==summary[1,1] && covidData[i,66]==summary[1,2]) 
  {summary[1,3]<-summary[1,3]+covidData$new_cases[i]
  summary[1,4]<-summary[1,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[2,1] && covidData[i,66]==summary[2,2]) 
  {summary[2,3]<-summary[2,3]+covidData$new_cases[i]
  summary[2,4]<-summary[2,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[3,1] && covidData[i,66]==summary[3,2]) 
  {summary[3,3]<-summary[3,3]+covidData$new_cases[i]
  summary[3,4]<-summary[3,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[4,1] && covidData[i,66]==summary[4,2]) 
  {summary[4,3]<-summary[4,3]+covidData$new_cases[i]
  summary[4,4]<-summary[4,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[5,1] && covidData[i,66]==summary[5,2]) 
  {summary[5,3]<-summary[5,3]+covidData$new_cases[i]
  summary[5,4]<-summary[5,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[6,1] && covidData[i,66]==summary[6,2]) 
  {summary[6,3]<-summary[6,3]+covidData$new_cases[i]
  summary[6,4]<-summary[6,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[7,1] && covidData[i,66]==summary[7,2]) 
  {summary[7,3]<-summary[7,3]+covidData$new_cases[i]
  summary[7,4]<-summary[7,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[8,1] && covidData[i,66]==summary[8,2]) 
  {summary[8,3]<-summary[8,3]+covidData$new_cases[i]
  summary[8,4]<-summary[8,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[9,1] && covidData[i,66]==summary[9,2]) 
  {summary[9,3]<-summary[9,3]+covidData$new_cases[i]
  summary[9,4]<-summary[9,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[10,1] && covidData[i,66]==summary[10,2]) 
  {summary[10,3]<-summary[10,3]+covidData$new_cases[i]
  summary[10,4]<-summary[10,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[11,1] && covidData[i,66]==summary[11,2]) 
  {summary[11,3]<-summary[11,3]+covidData$new_cases[i]
  summary[11,4]<-summary[11,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[12,1] && covidData[i,66]==summary[12,2]) 
  {summary[12,3]<-summary[12,3]+covidData$new_cases[i]
  summary[12,4]<-summary[12,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[13,1] && covidData[i,66]==summary[13,2]) 
  {summary[13,3]<-summary[13,3]+covidData$new_cases[i]
  summary[13,4]<-summary[13,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[14,1] && covidData[i,66]==summary[14,2]) 
  {summary[14,3]<-summary[14,3]+covidData$new_cases[i]
  summary[14,4]<-summary[14,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[15,1] && covidData[i,66]==summary[15,2]) 
  {summary[15,3]<-summary[15,3]+covidData$new_cases[i]
  summary[15,4]<-summary[15,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[16,1] && covidData[i,66]==summary[16,2]) 
  {summary[16,3]<-summary[16,3]+covidData$new_cases[i]
  summary[16,4]<-summary[16,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[17,1] && covidData[i,66]==summary[17,2]) 
  {summary[17,3]<-summary[17,3]+covidData$new_cases[i]
  summary[17,4]<-summary[17,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[18,1] && covidData[i,66]==summary[18,2]) 
  {summary[18,3]<-summary[18,3]+covidData$new_cases[i]
  summary[18,4]<-summary[18,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[19,1] && covidData[i,66]==summary[19,2]) 
  {summary[19,3]<-summary[19,3]+covidData$new_cases[i]
  summary[19,4]<-summary[19,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[20,1] && covidData[i,66]==summary[20,2]) 
  {summary[20,3]<-summary[20,3]+covidData$new_cases[i]
  summary[20,4]<-summary[20,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[21,1] && covidData[i,66]==summary[21,2]) 
  {summary[21,3]<-summary[21,3]+covidData$new_cases[i]
  summary[21,4]<-summary[21,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[22,1] && covidData[i,66]==summary[22,2]) 
  {summary[22,3]<-summary[22,3]+covidData$new_cases[i]
  summary[22,4]<-summary[22,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[23,1] && covidData[i,66]==summary[23,2]) 
  {summary[23,3]<-summary[23,3]+covidData$new_cases[i]
  summary[23,4]<-summary[23,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[24,1] && covidData[i,66]==summary[24,2]) 
  {summary[24,3]<-summary[24,3]+covidData$new_cases[i]
  summary[24,4]<-summary[24,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[25,1] && covidData[i,66]==summary[25,2]) 
  {summary[25,3]<-summary[25,3]+covidData$new_cases[i]
  summary[25,4]<-summary[25,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[26,1] && covidData[i,66]==summary[26,2]) 
  {summary[26,3]<-summary[26,3]+covidData$new_cases[i]
  summary[26,4]<-summary[26,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[27,1] && covidData[i,66]==summary[27,2]) 
  {summary[27,3]<-summary[27,3]+covidData$new_cases[i]
  summary[27,4]<-summary[27,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[28,1] && covidData[i,66]==summary[28,2]) 
  {summary[28,3]<-summary[28,3]+covidData$new_cases[i]
  summary[28,4]<-summary[28,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[29,1] && covidData[i,66]==summary[29,2]) 
  {summary[29,3]<-summary[29,3]+covidData$new_cases[i]
  summary[29,4]<-summary[29,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[30,1] && covidData[i,66]==summary[30,2]) 
  {summary[30,3]<-summary[30,3]+covidData$new_cases[i]
  summary[30,4]<-summary[30,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[31,1] && covidData[i,66]==summary[31,2]) 
  {summary[31,3]<-summary[31,3]+covidData$new_cases[i]
  summary[31,4]<-summary[31,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[32,1] && covidData[i,66]==summary[32,2]) 
  {summary[32,3]<-summary[32,3]+covidData$new_cases[i]
  summary[32,4]<-summary[32,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[33,1] && covidData[i,66]==summary[33,2]) 
  {summary[33,3]<-summary[33,3]+covidData$new_cases[i]
  summary[33,4]<-summary[33,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[34,1] && covidData[i,66]==summary[34,2]) 
  {summary[34,3]<-summary[34,3]+covidData$new_cases[i]
  summary[34,4]<-summary[34,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[35,1] && covidData[i,66]==summary[35,2]) 
  {summary[35,3]<-summary[35,3]+covidData$new_cases[i]
  summary[35,4]<-summary[35,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[36,1] && covidData[i,66]==summary[36,2]) 
  {summary[36,3]<-summary[36,3]+covidData$new_cases[i]
  summary[36,4]<-summary[36,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[37,1] && covidData[i,66]==summary[37,2]) 
  {summary[37,3]<-summary[37,3]+covidData$new_cases[i]
  summary[37,4]<-summary[37,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[38,1] && covidData[i,66]==summary[38,2]) 
  {summary[38,3]<-summary[38,3]+covidData$new_cases[i]
  summary[38,4]<-summary[38,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[39,1] && covidData[i,66]==summary[39,2]) 
  {summary[39,3]<-summary[39,3]+covidData$new_cases[i]
  summary[39,4]<-summary[39,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[40,1] && covidData[i,66]==summary[40,2]) 
  {summary[40,3]<-summary[40,3]+covidData$new_cases[i]
  summary[40,4]<-summary[40,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[41,1] && covidData[i,66]==summary[41,2]) 
  {summary[41,3]<-summary[41,3]+covidData$new_cases[i]
  summary[41,4]<-summary[41,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[42,1] && covidData[i,66]==summary[42,2]) 
  {summary[42,3]<-summary[42,3]+covidData$new_cases[i]
  summary[42,4]<-summary[42,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[43,1] && covidData[i,66]==summary[43,2]) 
  {summary[43,3]<-summary[43,3]+covidData$new_cases[i]
  summary[43,4]<-summary[43,4]+covidData$new_deaths[i]}
if (covidData[i,3]==summary[44,1] && covidData[i,66]==summary[44,2]) 
  {summary[44,3]<-summary[44,3]+covidData$new_cases[i]
  summary[44,4]<-summary[44,4]+covidData$new_deaths[i]}
}

#Plot chart of cases
barplot(summary,height = summary$cases,beside = TRUE)

#Creat function to calculate stats
generateDescStats<-function(v)
{
  #Initialise a blank vector to store values
  vDescStats<-NULL
  vDescStats<-c(vDescStats, mean(v, na.rm=TRUE)) #Use in built R Function
  vDescStats<-c(vDescStats, median(v, na.rm=TRUE)) #Use in built R Function
  vDescStats<-c(vDescStats, max(v, na.rm=TRUE)) #Use in built R Function
  vDescStats<-c(vDescStats, min(v, na.rm=TRUE)) #Use in built R Function
  vRange<-range(v, na.rm=TRUE) #Use in built R Function
  vDescStats<-c(vDescStats, vRange[2]-vRange[1]) 
  vDescStats<-c(vDescStats,sd(v, na.rm = TRUE)) #Use in built R Function
  
  # Return vDescStats for use in other script areas
  return(vDescStats)
}

#Create blank covidSummary data frame for later population
covidSummary<-data.frame(Mean=numeric(),
                         Median=numeric(),Max=numeric(),Min=numeric(),
                         Range=numeric(),StandardDev=numeric())

#Call generateDescStats function to create stats for expected months
UKApril20<-generateDescStats(covidData$new_cases[62:91])
UKOct20<-generateDescStats(covidData$new_cases[245:275])
UKApril21<-generateDescStats(covidData$new_cases[427:456])
UKOct21<-generateDescStats(covidData$new_cases[610:640])
ChinaApril20<-generateDescStats(covidData$new_cases[711:740])
ChinaOct20<-generateDescStats(covidData$new_cases[894:924])
ChinaApril21<-generateDescStats(covidData$new_cases[1076:1105])
ChinaOct21<-generateDescStats(covidData$new_cases[1259:1289])

#Use rbind to combine all statistics into one data frame
covidSummary<-rbind(covidSummary,UKApril20)
covidSummary<-rbind(covidSummary,UKOct20)
covidSummary<-rbind(covidSummary,UKApril21)
covidSummary<-rbind(covidSummary,UKOct21)
covidSummary<-rbind(covidSummary,ChinaApril20)
covidSummary<-rbind(covidSummary,ChinaOct20)
covidSummary<-rbind(covidSummary,ChinaApril21)
covidSummary<-rbind(covidSummary,ChinaOct21)

#Use cbind to assign a country and month to the existing data frame
covidSummary<-cbind(c('UK','UK','UK','UK','China','China','China','China')
                    ,c('April20','October20','April21','October21','April20','October20','April21','October21')
                    ,covidSummary)

#Rename columns to more reader friendly format
colnames(covidSummary)<-c('Country','Month','Mean','Median','Max','Min','Range','StandardDev')

#Use T-test to show significant difference between UK Oct 20 and UK Oct 21
#create vectors for Oct 20 and Oct 21 for use in analysis
Oct20<-covidData$new_cases[245:275]
Oct21<-covidData$new_cases[610:640]

#Use Shapiro to see if normally distributed
shapiro.test(Oct20)
shapiro.test(Oct21)

#As both results have a p value >0.05 we can assume data is normally distributed
#H0-There is no significant difference between new cases in selected months
#H1- There is a statisically significant difference between new cases
t.test(Oct20,Oct21)

#As p<0.05 we cannot reject the H0 and therefore there is no significant difference in new cases