File:Koronaviruksen R0 Suomessa 3.svg
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Summary
[edit]DescriptionKoronaviruksen R0 Suomessa 3.svg |
Suomi: Koronaviruksen perusuusitumisluku R0 keväällä 2020 Suomessa.
R0:n arvo saatata olla hieman yläkanttiin.
English: R0 of Covid-19 in Finland, spring 2020 |
Date | |
Source | Own work |
Author | Merikanto |
maybe inaccuray in actual "R0" value.
Source of data is aggregated COVID-19 dataset on net
https://datahub.io/core/covid-19/r/countries-aggregated.csv
System to calculate R0 is R0 package in "R".
Script to produce this image
- COVID-19 data refch && r0 calculation
- with R0 package
- data fetch from github COVID-19 data site
- additional script only, maybe needs adjust
- v 0001.0003
- 30.5.2021
-
- install.packages("ggplot2", "r0", "svglite",repos ="https://ftp.acc.umu.se/mirror/CRAN/")
library (R0)
library (ggplot2)
library(svglite)
- adjustables
library(svglite)
library(rvest)
library(readtext)
library(stringi)
library(stringr)
library(datamart)
library(XML)
library(jsonlite)
plotname<-"R0_Suomessa_3.svg" ## name of plot file
polku<-"../" ## path of plot file
yala=0.6
yyla=1.4
beginday1='01/04/2020'
- limits of input data
datelimits1=c('2020/04/01', '2020/04/25')
- dates of prediction
datelimits2=c('2020/04/01', '2021/05/28')
load_data_from=3
- 0, 1 or 2 , 0 none plot, 1 plot, 2 ggplot, -1 debug
plottaa<-1
levylle<-1 ## 0 to display, 1 to disc
plotname<-"R0_Suomessa_3.svg" ## name of plot file
polku<-"/Users/himot/akor1/" ## path of plot file
- today=Sys.Date()
- jos ylläoleva ei toimi, niin tää
- if above not func, this
today=Sys.Date()-1
- print(today)
today1=format(today, "%d/%m/%Y")
today2=format(today, "%Y/%m/%d")
- print(today1)
- print(today2)
- stop(-1)
datelimits1=c(beginday1, today1)
paivat1=seq(as.Date("2020/4/1"), as.Date(today2), "days")
load_data_from_finnish_wiki<-function()
{
url1="https://fi.wikipedia.org/wiki/Suomen_koronaviruspandemian_aikajana"
destfile1="./ward0.txt"
download.file(url1, destfile1)
texti000<-readtext(destfile1)
texti0<-texti000$text
etsittava1="1. huhtikuuta 2020 alkaen"
len1=nchar(texti0)
k1=regexpr(pattern=etsittava1, texti0)
k1b=len1-k1
texti1=strtail(texti0,k1b)
sink("out1.txt")
print (texti1)
sink()
etsittava2=""
k2=regexpr(pattern=etsittava2, texti1)
texti2=strhead(texti1,k2)
sample1<-minimal_html(texti2)
tabu1 <- html_table(sample1, fill=TRUE)1
colnames(tabu1) <- c("V1","V2", "V3","V4", "V5","V6", "V7","V8" )
- print(tabu1)
sairaalassa00<-tabu1$V4
sairaalassa=as.integer(sairaalassa00)
teholla00<-tabu1$V5
teholla=as.integer(teholla00)
uusiatapauksia00<-tabu1$V3
uusiatapauksia0<-gsub(" ", "", uusiatapauksia00)
uusia_tapauksia=as.integer(uusiatapauksia0)
uusiakuolleita00<-tabu1$V7
uusiakuolleita1=as.integer(uusiakuolleita00)
uusiakuolleita2<-uusiakuolleita1
uusiakuolleita2[uusiakuolleita2<0]<-0
uusia_kuolleita<-uusiakuolleita2
toipuneita00<-tabu1$V8
toipuneita01<-gsub(" ", "", toipuneita00)
toipuneita0<-gsub("[^0-9.-]", "", toipuneita01)
toipuneita=as.integer(toipuneita0)
tapauksia00<-tabu1$V2
tapauksia01<-gsub(" ", "", tapauksia00)
tapauksia0<-gsub("[^0-9.-]", "", tapauksia01)
tapauksia=as.integer(tapauksia0)
kuolleita00<-tabu1$V6
kuolleita=as.integer(kuolleita00)
aktiivisia_tapauksia=tapauksia-kuolleita-toipuneita
- print (paivat1)
- print (teholla)
- print (sairaalassa)
- print (tapauksia)
- print (kuolleita)
- print (toipuneita)
- print (uusia_tapauksia)
- print (uusia_kuolleita)
- plot(paivat1,aktiivisia_tapauksia)
- xy<-data.frame(paivat1, sairaalassa)
xy<-data.frame(paivat1, uusia_tapauksia)
- xy<-data.frame(paivat1, tapauksia)
xyz<-data.frame(paivat1, sairaalassa, teholla)
dfout1<-data.frame(paivat1, aktiivisia_tapauksia, uusia_tapauksia, sairaalassa, teholla, uusia_kuolleita )
names(dfout1)<-c("Pvm", "Aktiivisia_tapauksia","Uusia_tapauksia", "Sairaalassa", "Teholla", "Uusia_kuolleita")
write.csv2(dfout1, "./sairaalassa.csv",row.names=FALSE )
return(xy)
}
load_data_from_aggregated<-function()
{
- fetch the data
dfine <- read.csv(file = 'https://datahub.io/core/covid-19/r/countries-aggregated.csv')
- head(dfine)
- class(dfine)
- tail(dfine, 5)
dfinland <- dfine[ which(dfine$Country=='Finland'), ]
- head(dfinland)
kols <- c("Date", "Confirmed","Recovered","Deaths")
tapaukset <- dfinland[kols]
- head(tapaukset)
len1=nrow(tapaukset)
- len1
len2=len1-1
len3=len2
confirmed<-tapaukset$Confirmed
deaths<-tapaukset$Deaths
dailycases <- vector()
dailycases <- c(dailycases, 0:(len2))
dailydeaths <- vector()
dailydeaths <- c(dailydeaths, 0:(len2))
m=0
dailycases[1]<-tapaukset$Confirmed[1]
- dailydeaths[1]<-tapaukset$Deaths[1]
dailydeaths[1]<-0
- confirmed
- deaths
m=1
for(n in 2:(len3+1)) {
a<-confirmed[n]
b<-confirmed[m]
#print (a)
#print (b)
cee<- (a-b)
#print(cee)
dailycases[n]=cee
m=m+1
}
mm=1
for(nn in 2:(len3+1)) {
aa<-deaths[nn]
bb<-deaths[mm]
#print ("_")
#print (aa)
#print (bb)
ceb=aa-bb
#if (ceb<0) ceb=0
#print(ceb)
dailydeaths[nn]=ceb
mm=mm+1
}
- deaths
- dailycases
- dailydeaths
dfout1<-dfinland
- print(nrow(dfinland))
- print(length(dailydeaths))
dfout1 <- cbind(dfout1, data.frame(dailycases))
dfout1 <- cbind(dfout1, data.frame(dailydeaths))
- head(dfout1)
dfout2<-within(dfout1, rm(Country))
names(dfout2) <- c('Date','Confirmed','Recovered','Deaths', 'DailyConfirmed','DailyDeaths')
- head(dfout2)
write.csv2(dfout2, "/Users/himot/akor1/finland_data1.csv");
daate1<-dfout2$Date
dailydeaths1<-dfout2$DailyDeaths
dailycases1<-dailycases
- daate1
- daate2<-gsub("2020-", "", daate1)
daate2<-daate1
leenu<-length(daate2)
- alkupvm<-50
alkupvm<-1
daate3<-daate2[alkupvm:leenu]
dailydeaths3<-dailydeaths1[alkupvm:leenu]
dailycases3<-dailycases1[alkupvm:leenu]
- daate3
- dailydeaths3
# barplot(dailydeaths3, main="Koronaviruskuolemat päivittäin vuonna 2020",
# names.arg=daate3)
dataf1 <- data.frame("Date" = daate3, "Paivitt_kuolemat"=dailydeaths3)
- str(dataf1)
dataf2 <- data.frame("Date" = daate3, "Paivitt_tapaukset"=dailycases3)
- str(dataf2)
write.csv(dataf1, "/Users/himot/akor1/dailydeaths1.csv", row.names=T)
write.csv(dataf2, "/Users/himot/akor1/dailycases1.csv", row.names=T)
indf1 <- read.csv(file = '/Users/himot/akor1/dailycases1.csv')
#head(indf1)
cases1<-indf1$Paivitt_tapaukset
dates1<-indf1$Date
len1=length(cases1)
dates2<-as.Date(dates1)
paivat<-1:len1
xy<-data.frame(daate3, dailycases3)
}
download_solanpaa_finnish_data<-function()
{
solanpaa_fi="https://covid19.solanpaa.fi/data/fin_cases.json"
cache_file="solanpaa_fi.json"
download.file(solanpaa_fi, cache_file)
j1 <- fromJSON(cache_file)
## maybe errori
dates<-as.Date(j1$date)
dailycases<-j1$new_cases
dailydeaths<-j1$new_deaths
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)
names(xy0)<-c("Dates", "Cases")
xy<-na.omit(xy0)
return(xy)
}
lataa_thl_tapaukset_kuolleet<-function()
{
url1<-"https://sampo.thl.fi/pivot/prod/fi/epirapo/covid19case/fact_epirapo_covid19case.json?row=measure-492118&column=dateweek20200101-508804L"
cube1 <- fromJSONstat(url1, naming = "label", use_factors = F, silent = T)
res01 <- cube11
#res00
url2<-"https://sampo.thl.fi/pivot/prod/fi/epirapo/covid19case/fact_epirapo_covid19case.json?row=measure-444833&column=dateweek20200101-508804L"
cube2 <- fromJSONstat(url2, naming = "label", use_factors = F, silent = T)
res02 <- cube21
#res02
#stop (-1)
paiva=as.Date(res01$dateweek20200101)
kuolleet=as.integer(res01$value)
tapaukset=as.integer(res02$value)
kuolin_prosentit=kuolleet/tapaukset
kuolin_prosentit=kuolin_prosentit*10000
kuolin_prosentit=as.integer(kuolin_prosentit)
kuolin_prosentit=as.double(kuolin_prosentit)
kuolin_prosentit=kuolin_prosentit/100.0
#print (paiva)
#print (kuolleet)
#stop(-1)
#print (tapaukset)
#print (kuolin_prosentit )
df1<-data.frame(paiva,tapaukset, kuolleet, kuolin_prosentit)
names(df1)<-c("Paiva", "Tapauksia", "Kuolleita", "Kuolinprosentti")
#write.csv2(df1, "./kuolleet_ikaryhmittain.csv", sep = ";" )
write.csv(df1, "./thl_tapaukset_kuolleet.csv")
xy0<-data.frame(paiva, tapaukset)
names(xy0)<-c("Dates", "Cases")
xy<-na.omit(xy0)
#return(df1)
}
- main program
if(load_data_from==1)
{
xy<-load_data_from_finnish_wiki()
print (xy)
}
if(load_data_from==2)
{
xy<-load_data_from_aggregated()
}
if(load_data_from==3)
{
xy<-download_solanpaa_finnish_data()
}
if(load_data_from==4)
{
xy<-lataa_thl_tapaukset_kuolleet()
}
names(xy)<-c("Dates","Cases")
select_datelimit_begin=as.Date(beginday1,format="%d/%m/%Y")
select_datelimit_end=as.Date(today1)
xy2<-xy[xy$Dates >= select_datelimit_begin,]
#print(xy2)
- stop(-1)
cases1<-xy2$Cases
dates1<-xy2$Dates
xy3<-data.frame( as.Date(dates1),as.integer(cases1) )
names(xy3)<-c("Dates", "Cases")
len1=length(cases1)
dates2<-as.Date(dates1)
paivat<-1:len1
num1<-cases1
dates1<-dates1
names1=dates1
len1=length(num1)
alku<-as.integer(len1*0+1)
loppu<-as.integer(len1)
start_lok<-as.integer(1)
end_lok<-as.integer(len1)
paivat<-as.Date(dates1[start_lok:(end_lok)])
indexes1=start_lok:end_lok
num1[is.na(num1)] <- 1
num1[(num1<0)] <- num1*-1
num1[num1==0] <- 1
num<-num1[start_lok:end_lok]
- names<-names1[start_lok:end_lok]
- names<-indexes1
names<-paivat
df1 <- setNames(num, names)
str(df1)
koedata<-as.integer((rnorm(len1)+1)*100)+300
- koedata[(koedata<0)] <- koedata
koedata
- num<-koedata
df2<- setNames(num, names)
- df1
mgt = generation.time ("gamma", c(3, 1.5))
- mgt = generation.time ("gamma", c(6, 0.5))
- TD <- estimate.R(df1, mgt, begin=start_lok, end=end_lok, methods="TD", nsim=100)
- TD <- estimate.R(df1, mgt, begin=1, end=166, methods="TD", nsim=1000)
- teda<- estimate.R(df1, mgt, begin=1, end=166, methods="EG", nsim=600)
- teda<- estimate.R(df1, mgt, begin=1, end=166,methods="TD", nsim=600)
- teda<-est.R0.EG (df1, mgt,begin=1, end=166, methods="TD" , nsim=600)
teda <- estimate.R(df1, mgt, begin=alku, end=loppu, methods="TD", nsim=2000)
str(teda)
teda$R
r0t1<-teda$estimates$TD$R
conf1<-teda$conf.int
r0t1[is.na(r0t1)] <- 1
length(paivat)
length(r0t1)
xy<-data.frame(paivat, r0t1)
- names(xy)<-c("names", "num")
tee5 <- smooth.Rt(teda$estimates$TD, 3)
- TD.5D <- smooth.Rt(TD$estimates$TD, 1)
tee5
str(tee5)
aika5<-tee5$epid$t
yla5<-tee5$conf.int$lower
ala5<-tee5$conf.int$upper
keski5<-((ala5+yla5)/2)
pvm1= as.Date(aika5, "%Y-%m-%d")
if(plottaa==-1)
{
plot(pvm1, keski5)
}
if(plottaa==1)
{
print("")
print("Ggplot")
print("")
if(levylle==1)
{
plotname1<-paste0(polku, plotname)
#svg(filename=plotname1, width=6, height=3, pointsize=12)
}
gee<- ggplot(xy, aes(x =paivat , y = r0t1)) +
theme_minimal()+
#geom_point()+
ylim(yala, yyla)+
ggtitle("Arvioitu koronaviruksen perusuusiutumisluku R0") +
xlab("Kuukausi") + ylab("R0")+
theme(title=element_text(size=15), axis.text=element_text(size=12,face="bold"),axis.title=element_text(size=14,face="bold"))+
geom_line()+
#geom_point() +
geom_smooth( fill="#a0a0ff",level=0.99, span=0.1)
#geom_smooth( fill="#9090ff", level=0.7) +
#geom_smooth( fill="#8a08af", level=0.5)
#Sys.sleep(5)
if(levylle==1)
{
ggsave(file=plotname1, plot=gee, width=10, height=4)
dev.off()
}
}
print("->.")
Licensing
[edit]- You are free:
- to share – to copy, distribute and transmit the work
- to remix – to adapt the work
- Under the following conditions:
- attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- share alike – If you remix, transform, or build upon the material, you must distribute your contributions under the same or compatible license as the original.
File history
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Date/Time | Thumbnail | Dimensions | User | Comment | |
---|---|---|---|---|---|
current | 08:15, 9 August 2021 | 512 × 205 (20 KB) | Merikanto (talk | contribs) | Update | |
12:43, 30 May 2021 | 512 × 205 (19 KB) | Merikanto (talk | contribs) | Update | ||
08:10, 26 April 2021 | 512 × 205 (19 KB) | Merikanto (talk | contribs) | Update atyempt | ||
12:27, 23 March 2021 | 810 × 360 (60 KB) | Merikanto (talk | contribs) | Upload | ||
14:41, 11 January 2021 | 810 × 360 (57 KB) | Merikanto (talk | contribs) | Update | ||
13:39, 3 December 2020 | 810 × 360 (58 KB) | Merikanto (talk | contribs) | Upload | ||
11:52, 4 November 2020 | 810 × 360 (57 KB) | Merikanto (talk | contribs) | Update | ||
12:26, 18 September 2020 | 810 × 360 (54 KB) | Merikanto (talk | contribs) | Update | ||
13:44, 2 September 2020 | 810 × 360 (54 KB) | Merikanto (talk | contribs) | Update | ||
15:07, 14 August 2020 | 810 × 360 (54 KB) | Merikanto (talk | contribs) | Update of data in curve |
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