1. 3. Download Covid-19 data from Finnish Wikipedia
   5. "R" script
   6. New cases, new deaths, ward, icu, active cases ...
      1. plot ward, icu, daily deaths
   8. draft version 0003.0003
2. 5.6.2021

2. install.packages("rvest")
3. install.packages("readtext")
4. install.packages("stringi")
5. install.packages("datamart")
6. install.packages("XML")
7. install.packages("svglite")
8. install.packages("ggplot2")
9. install.packages("tidyr")
10. install.packages("stringr")
11. install.packages("stringi")
12. install.packages("tibble")

library(rvest) library(readtext) library(stringi) library(datamart) library(XML) library(ggplot2) library(tidyr) library(stringr) library(stringi) library(tibble)

library(XML) library(jsonlite)

1. 1. NOTE date limits change this

1. datelimits1=c('1/3/2020', '9/11/2020')
   1. display date limits

beginday1='1/1/2021'

today=Sys.Date() yesterday=today-1

yesterday=today

rajapaiva=yesterday

1. print(today)
2. print (yesterday)

1. stop(-1)

1. today1=format(today, "%d/%m/%Y")
2. today2=format(today, "%Y/%m/%d")

rajapaiva1=format(rajapaiva, "%d/%m/%Y") rajapaiva2=format(rajapaiva, "%Y/%m/%d")

1. print(today1)
2. print(today2)

1. stop(-1)

1. datelimits1=c(beginday1, today1)

datelimits1=c(beginday1, rajapaiva1)

1. 1. dates of dataset

paivat1=seq(as.Date("2020/4/1"), as.Date(rajapaiva2), "days")

plottaa=1 ## must be 1

1. 1. 1 : ward, icu 2 : ward, active infections
   2. 3 ward, icu, deaths

tulosta_svg=2 # plot to out svg 0, 1 of 2

1. 1. smooth curves pars
2. spanni=0.2

spanni=0.2 metodi="loess"

filename1="./koronan_takia_sairaalassa_ja_teholla_1.svg"

download_solanpaa_finnish_data<-function() {

solanpaa_fi="https://covid19.solanpaa.fi/data/fin_cases.json" cache_file="solanpaa_fi.json"

download.file(solanpaa_fi, cache_file)

j1 <- fromJSON(cache_file)

#print(j1)

 ## maybe errori

dates<-as.Date(j1$date)

dailycases<-j1['new_cases'] dailydeaths<-j1['new_deaths'] hospital<-j1['hospitalized'] icu<-j1['in_icu']

   dataf1 <- data.frame("Date" = dates, "Paivitt_kuolemat"=dailydeaths) 
   dataf2 <- data.frame("Date" = dates, "Paivitt_tapaukset"=dailycases)

write.csv(dataf1, "./dailydeaths1.csv", row.names=T) write.csv(dataf2, "./dailycases1.csv", row.names=T)

xy0<-data.frame(dates, dailycases,dailydeaths, hospital, icu) names(xy0)<-c("Dates", "Daily_cases", "Daily_deaths","Hospital", "Icu" ) xy<-na.omit(xy0) print("Solanpää data")

return(xy)

}

xy<-download_solanpaa_finnish_data()

paivat1<-xy$Dates uusia_tapauksia<-xy$Daily_cases uusia_kuolleita<-xy$Daily_deaths sairaalassa<-xy$Hospital teholla<-xy$Icu

uusia_tapauksia[uusia_tapauksia<0] <- 0 uusia_kuolleita[uusia_kuolleita<0] <- 0

1. stop(-1)
2. quit(-1)

xy<-data.frame(paivat1, sairaalassa) xyz<-data.frame(paivat1, sairaalassa, teholla)

1. dfout1<-data.frame(paivat1, aktiivisia_tapauksia, uusia_tapauksia, sairaalassa, teholla, uusia_kuolleita )

dfout1<-data.frame(paivat1, sairaalassa, teholla, uusia_kuolleita, uusia_tapauksia )

names(dfout1)<-c("Pvm", "Sairaalassa", "Teholla", "Uusia_kuolleita","Uusia_tapauksia")

write.csv2(dfout1, "./sairaalassa.csv",row.names=FALSE )

if(tulosta_svg==2) { svg(filename=filename1, width=14, height=6, pointsize=12) #svg(filename=filename1, width=10, height=6, pointsize=12) #svg(filename=filename1, width=14, height=6, pointsize=12) }

if (plottaa==1) {

print ("Sairaalassa teholla päivittäiset kuolemat")

coeff <- 15

ylim.prim <- c(0, 100) ylim.sec <- c(0, 10)

b <- diff(ylim.prim)/diff(ylim.sec) a <- b*(ylim.prim[1] - ylim.sec[1])

#stop(-1)

dfm<-data.frame(paivat1, uusia_tapauksia, sairaalassa, teholla, uusia_kuolleita)

#dfm2<-data.frame(paivat1, uusia_tapauksia, sairaalassa, teholla)

# ggplot(dfm, aes(x=paivat1), color="Potilaita", fill="Potilaita") + # geom_line(aes(y=sairaalassa, color="Sairaalassa"), size=2)+ # geom_line(aes(y=teholla, color="Teholla"), size=2)+ # geom_col( aes(y=uusia_kuolleita, color="Uusia kuolleita"), size=2)+ # scale_color_manual(name="Potilaita",breaks = c("Sairaalassa", "Teholla", "Uusia kuolleita"), # values=c("orange","red", "black") )

 	ggplot(dfm, aes(x=paivat1), color="Potilaita", fill="Potilaita") +
 	xlim(as.Date(datelimits1, format="%d/%m/%Y") )+
   theme_light()+
 	geom_col(aes(y= a + uusia_kuolleita*b, color="Uusia kuolleita"), fill="black",size=2)+

geom_line(aes(y=sairaalassa, color="Sairaalassa"),fill="white", size=2)+ geom_line(aes(y=teholla, color="Teholla"), fill="white",size=2)+ scale_y_continuous("Sairaalassa/teholla", sec.axis = sec_axis(~ (. - a)/b, name = "Kuolleita/pv")) +

scale_color_manual(name="Potilaita",breaks = c("Sairaalassa", "Teholla", "Uusia kuolleita"),

                       values=c("orange","red", "black") ) +
  	#scale_fill_manual(name="Potilaita",breaks = c("Sairaalassa", "Teholla", "Uusia kuolleita"),
   #                    values=c("orange","red", "black") ) +                     
                       
   ggtitle("Koronan takia sairaalassa - 2021") +

xlab("Kuukausi") +

   theme(axis.line.y.right = element_line(color = "black"), 

axis.ticks.y.right = element_line(color = "black"), axis.text.y.right = element_text(color = "black"), axis.title.y.right = element_text(color = "black")

       ) +
    
    		theme(axis.line.y.left = element_line(color = "darkred"), 

axis.ticks.y.left = element_line(color = "darkred"), axis.text.y.left = element_text(color = "darkred"), axis.title.y.left = element_text(color = "darkred")

       ) +
       
       theme(title=element_text(size=18, face="bold"), 

axis.text=element_text(size=18,face="bold"), axis.title=element_text(size=18,face="bold"), legend.title=element_text(size=18, face="bold"), legend.text=element_text(size=18, face="bold") )

}

if(tulosta_svg==2) { dev.off() print("Ggplot svg done.") }