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covid2.R
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covid2.R
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library(zoo)
#library(numbers)
#library(plotly)
#library(plyr)
#library(lubridate)
#library(drc)
######################################################################
rm(list=ls(all=TRUE))
graphics.off()
cat("\014")
######################################################################
load("covid_data.Rdata");
#WINDOW SIZE:
WINDOWS_SIZE=7
width1=1100
height1=600
countries <-c('Greece','Sweden','Italy','Serbia','Croatia','Bosnia and Herzegovina','Bulgaria','Belgium','Albania','Romania','Spain','Portugal','United Kingdom','France');
#cidx <- function(cname){
# match(cname,countries);
#}
#'greece','sweden','italy','serbia','croatia','bosnia','bulgaria','belgium'
population <- list();
population['Sweden']<-10099265 #worldometers2020
population['Italy']<-60461826 #worldometers2020
population['Greece']<-10423054 #worldometers2020
population['Serbia']<-8737371 #worldometers2020
population['Croatia']<-4105267 #worldometers2020
population['Bosnia and Herzegovina']<-3280819 #worldometers2020
population['Bulgaria']<-6948445 #worldometers2020
population['Belgium']<-11589623 #worldometers2020
population['Albania']<-2877797 #worldometers2020
population['Romania']<-19237691 #worldometers2020
population['Spain']<-46754778 #worldometers2020
population['Portugal']<-10196709 #worldometers2020
population['United Kingdom'] <- 67886011 #worldometers2020
population['France'] <- 65273511 #worldometers2020
#'greece','sweden','italy','serbia','croatia','bosnia','bulgaria'
eng_all <- covid_all[covid_all$country.region%in%"United Kingdom",];
fra_all <- covid_all[covid_all$country.region%in%"France",]
covid = list(
covid_all[covid_all$country.region%in%"Greece",],
covid_all[covid_all$country.region%in%"Sweden",],
covid_all[covid_all$country.region%in%"Italy",],
covid_all[covid_all$country.region%in%"Serbia",],
covid_all[covid_all$country.region%in%"Croatia",],
covid_all[covid_all$country.region%in%"Bosnia and Herzegovina",],
covid_all[covid_all$country.region%in%"Bulgaria",],
covid_all[covid_all$country.region%in%"Belgium",],
covid_all[covid_all$country.region%in%"Albania",],
covid_all[covid_all$country.region%in%"Romania",],
covid_all[covid_all$country.region%in%"Spain",],
covid_all[covid_all$country.region%in%"Portugal",],
eng_all[eng_all$province.state%in%"",],
fra_all[fra_all$province.state%in%"",]
#covid_all[covid_all$country.region%in%"France",]
);
names(covid)<- countries;
#summary(covid)
#counties_all<-unique(covid_all$country.region)
#eng1=covid_all[covid_all$country.region%in%"United Kingdom",] ;
#eng2<-eng1[eng1$province.state%in%"",]
#covid[['greece']]$confirmed
#covid$greece$confirmed
perc<-100
for (i in countries){
covid[[i]]$confirmed_r <- (covid[[i]]$confirmed /population[[i]])*perc
}
for (i in countries){
covid[[i]]$deaths_r <- (covid[[i]]$deaths /population[[i]])*perc
}
for (i in countries){
covid[[i]]$fatality_r <- (covid[[i]]$deaths / covid[[i]]$confirmed)*perc
}
fn_roll1 <- function(w){
len<-length(w);
r <- rep(NA, len-1)
for (i in seq(len,2,by=-1)){
j = i-1;
r[j]<- w[i]-w[j];
}
#return (sum(r)/(len-1))
return (sum(r))
}
fn_roll2 <- function(w){
#cat(w,"\n")
len <- length(w)
r<- w[len]
return (r)
}
wsize <- WINDOWS_SIZE+1
covid_w <- list();
for (i in countries){
covid_w[[i]]$deaths <- rollapply(covid[[i]]$deaths,wsize,fn_roll1)
covid_w[[i]]$fatality <- rollapply(covid[[i]]$fatality,wsize,fn_roll1)
covid_w[[i]]$confirmed <- rollapply(covid[[i]]$confirmed,wsize,fn_roll1)
covid_w[[i]]$deaths_r <- rollapply(covid[[i]]$deaths_r,wsize,fn_roll1)
covid_w[[i]]$fatality_r <- rollapply(covid[[i]]$fatality_r,wsize,fn_roll1)
covid_w[[i]]$confirmed_r <- rollapply(covid[[i]]$confirmed_r,wsize,fn_roll1)
covid_w[[i]]$date <- rollapply(covid[[i]]$date,wsize,fn_roll2)
}
covid_greece<-list();
covid_greece$date <- covid[['Greece']]$date
covid_greece$deaths <- covid[['Greece']]$deaths
covid_greece$fatality_r <- covid[['Greece']]$fatality_r
covid_greece$confirmed <- covid[['Greece']]$confirmed
#covid_greece_w<-list();
covid_greece$w_deaths <- rollapply(covid[['Greece']]$deaths,2,fn_roll1)
covid_greece$w_confirmed <- rollapply(covid[['Greece']]$confirmed,2,fn_roll1)
covid_greece$w_date <- rollapply(covid[['Greece']]$date,2,fn_roll2)
#names(covid_w)
#names(covid_w[['greece']])
#length(covid_w[['greece']]$date)
#length(covid_w[['greece']]$deaths)
#length(covid[['greece']]$date)
#length(covid[['greece']]$deaths)
plot1 <- function(var_name, fname,title, country,color,max_default=0){
cat('plot1:',var_name,',',fname,',',title,"\n")
maxv <- 0;
if (max_default == 0){
for (i in country){
#cat(':',covid[[i]][[var_name]],"\n");
maxv <- max(maxv, max(covid[[i]][[var_name]],na.rm=TRUE))
}
} else {
maxv <- max_default
}
#cat("max:",maxv,"\n")
#clen = length(country);
fname_f <- paste('target','/',fname,'.png', sep='' )
png(file=fname_f,width=width1,height=height1)
main_title <- paste(title,'απο την αρχή της πανδημίας' )
c <-0;
for (i in country){
c <- c +1;
dates<-covid[[i]]$date
#for (dd in dates){
# cat(dd)
#}
if (c == 1){
plot(dates, covid[[i]][[var_name]],col=color[c],
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=main_title,xlab='time',ylab=title, type="l", ylim=c(0,maxv))
} else {
lines(lwd=1.3, dates, covid[[i]][[var_name]],col=color[c])
}
}
legend(x="topleft",
legend=country,
col=color,
lty=1,
pch=NA ,
lwd=3,
cex=1.8)
grid()
dev.off()
maxv <- 0;
for (i in country){
#cat(':',covid_w[[i]][[var_name]],"\n");
maxv <- max(maxv, max(covid_w[[i]][[var_name]],na.rm=TRUE))
}
fname_f <- paste('target','/',fname,'_w.png', sep='' )
png(file=fname_f,width=width1,height=height1)
title = paste(title,' Ανα βδομάδα')
c <-0;
for (i in country){
c <- c +1;
dates <- base::as.Date(zoo::as.Date(covid_w[[i]]$date))
#dates <- covid_w[[i]]$date
if (c == 1){
plot(dates, covid_w[[i]][[var_name]],col=color[c],
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=title,xlab='time',ylab=title, type="l", ylim=c(0,maxv))
} else {
lines(lwd=1.3, dates, covid_w[[i]][[var_name]],col=color[c])
}
}
legend(x="topleft",
legend=country,
col=color,
lty=1,
pch=NA ,
lwd=3,
cex=1.8)
grid()
dev.off()
}
plot_countries0<-c('Greece')
plot_colors0<-c('black')
plot_countries1<-c('Greece','Italy','France')
plot_colors1<-c('black','blue','red')
plot_countries1a<-c('Greece','Sweden','United Kingdom')
plot_colors1a<-c('black','blue','red')
plot_countries2<-c('Greece','Croatia','Serbia')
plot_colors2<-c('black','blue','red')
plot_countries3<-c('Greece','Bulgaria','Bosnia and Herzegovina')
plot_colors3<-c('black','green','orange')
plot_countries4<-c('Greece','Romania','Albania')
plot_colors4<-c('black','green','orange')
plot_countries5<-c('Greece','Spain','Portugal')
plot_colors5<-c('black','green','orange')
#################################################
## DEATHS RATE
#################################################
title<-'θάνατοι %'
plot_var<-'deaths_r';
#plot_fname<-'covid_deaths'
#plot1(plot_var,plot_fname,title,plot_countries0,plot_colors0)
plot_fname<-'covid_deaths_gif'
plot1(plot_var,plot_fname,title,plot_countries1,plot_colors1)
plot_fname<-'covid_deaths_gus'
plot1(plot_var,plot_fname,title,plot_countries1a,plot_colors1a)
plot_fname<-'covid_deaths_gcs'
plot1(plot_var,plot_fname,title,plot_countries2,plot_colors2)
plot_fname<-'covid_deaths_gbb'
plot1(plot_var,plot_fname,title,plot_countries3,plot_colors3)
plot_fname<-'covid_deaths_gar'
plot1(plot_var,plot_fname,title,plot_countries4,plot_colors4)
plot_fname<-'covid_deaths_gsp'
plot1(plot_var,plot_fname,title,plot_countries5,plot_colors5)
#################################################
#################################################
## FATALITY RATE
#################################################
title<-'fatality %'
plot_var<-'fatality_r';
#plot_fname<-'covid_fatality'
#plot1(plot_var,plot_fname,title,plot_countries0,plot_colors0)
plot_fname<-'covid_fatality_gif'
plot1(plot_var,plot_fname,title,plot_countries1,plot_colors1)
plot_fname<-'covid_fatality_gus'
plot1(plot_var,plot_fname,title,plot_countries1a,plot_colors1a)
plot_fname<-'covid_fatality_gcs'
plot1(plot_var,plot_fname,title,plot_countries2,plot_colors2)
plot_fname<-'covid_fatality_gbb'
plot1(plot_var,plot_fname,title,plot_countries3,plot_colors3,6.7)
plot_fname<-'covid_fatality_gar'
plot1(plot_var,plot_fname,title,plot_countries4,plot_colors4)
plot_fname<-'covid_fatality_gsp'
plot1(plot_var,plot_fname,title,plot_countries5,plot_colors5)
#################################################
#################################################
## CONFIRMED RATE
#################################################
title<-'Επιβεβαιωμένα κρούσματα %'
plot_var<-'confirmed_r';
#plot_fname<-'covid_confirmed'
#plot1(plot_var,plot_fname,title,plot_countries0,plot_colors0)
plot_fname<-'covid_confirmed_gif'
plot1(plot_var,plot_fname,title,plot_countries1,plot_colors1)
plot_fname<-'covid_confirmed_gus'
plot1(plot_var,plot_fname,title,plot_countries1a,plot_colors1a)
plot_fname<-'covid_confirmed_gcs'
plot1(plot_var,plot_fname,title,plot_countries2,plot_colors2)
plot_fname<-'covid_confirmed_gbb'
plot1(plot_var,plot_fname,title,plot_countries3,plot_colors3)
plot_fname<-'covid_confirmed_gar'
plot1(plot_var,plot_fname,title,plot_countries4,plot_colors4)
plot_fname<-'covid_confirmed_gsp'
plot1(plot_var,plot_fname,title,plot_countries5,plot_colors5)
#################################################3
main_title<-'Ελλάδα θάνατοι απο την αρχή της πανδημίας'
y_title<-'θάνατοι'
png(file='target/covid_greece_deaths.png',width=width1,height=height1)
plot(covid_greece$date, covid_greece$deaths, col='black',
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=main_title,xlab='time',ylab=y_title, type="l")
grid()
dev.off()
main_title<-'Greece fatality %'
y_title<-'fatality %'
png(file='target/covid_greece_fatality.png',width=width1,height=height1)
plot(covid_greece$date, covid_greece$fatality_r, col='black',
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=main_title,xlab='time',ylab=y_title, type="l")
grid()
dev.off()
main_title<-'Ελλάδα επιβεβαιωμένα κρούσματα απο την αρχή της πανδημίας'
y_title<-'confirmed'
png(file='target/covid_greece_confirmed.png',width=width1,height=height1)
plot(covid_greece$date, covid_greece$confirmed, col='black',
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=main_title,xlab='time',ylab=y_title, type="l")
grid()
dev.off()
wdates <- base::as.Date(zoo::as.Date(covid_greece$w_date))
main_title<-'Ελλάδα επιβεβαιωμένα κρούσματα ανα ημέρα'
y_title<-'confirmed'
png(file='target/covid_greece_confirmed_w.png',width=width1,height=height1)
plot(wdates, covid_greece$w_confirmed, col='black',
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=main_title,xlab='time',ylab=y_title, type="l")
grid()
dev.off()
main_title<-'Ελλάδα θανάτοι ανα ημέρα'
y_title<-'deaths'
png(file='target/covid_greece_deaths_w.png',width=width1,height=height1)
plot(wdates, covid_greece$w_deaths, col='black',
lwd=1.3, cex=1.6, cex.lab=1.6, cex.main=1.6, cex.sub=1.6, cex.axis=1.6, main=main_title,xlab='time',ylab=y_title, type="l")
grid()
dev.off()