File:Koronaviruksen R0 Suomessa 4.svg
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[edit]DescriptionKoronaviruksen R0 Suomessa 4.svg |
Suomi: Koronaviruksen R0 Suomessa keväällä 2020. Musta käyrä: keskiarvo. Vihreä käyrä, mediaani. Yhtenäiset käyrät luottamusväli 25-75 prosenttia. Katkoviivat 5-95 prosenttia. Punaine yläraja, vihreä alaraja.
English: Black curve, mean estimate. Green curve, median estimate.
Continuous blue and red curves, 25-75 % confidence limits. Dashed curves 5% - 95 %confidence. Red uper limit, blue lower limit. |
Date | |
Source | Own work |
Author | Merikanto |
- calculate r0 of finnish covid epidemy
- "R" epiestim r0 test
-
- alpha edition
- v 0001.0003
- 30.5.2021
- install.packages("EpiEstim", repos ="https://ftp.acc.umu.se/mirror/CRAN/")
library(EpiEstim)
library(ggplot2)
library(svglite)
library(rvest)
library(readtext)
library(stringi)
library(stringr)
library(datamart)
library(XML)
library(zoo)
library(jsonlite)
beginday1='01/04/2020'
- limits of input data
datelimits1=c('2020/04/01', '2020/04/25')
- dates of prediction
datelimits2=c('2020/04/01', '2021/04/25')
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_4.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$value)
kuolin_prosentit=kuolleet/tapaukset
kuolin_prosentit=kuolin_prosentit*10000
kuolin_prosentit=as.integer(kuolin_prosentit)
kuolin_prosentit=as.double(kuolin_prosentit)
kuolin_prosentit=kuolin_prosentit/100.0
#print (paiva)
#print (kuolleet)
#stop(-1)
#print (tapaukset)
#print (kuolin_prosentit )
df1<-data.frame(paiva,tapaukset, kuolleet, kuolin_prosentit)
names(df1)<-c("Paiva", "Tapauksia", "Kuolleita", "Kuolinprosentti")
#write.csv2(df1, "./kuolleet_ikaryhmittain.csv", sep = ";" )
write.csv(df1, "./thl_tapaukset_kuolleet.csv")
xy0<-data.frame(paiva, tapaukset)
names(xy0)<-c("Dates", "Cases")
xy<-na.omit(xy0)
#return(df1)
}
if(load_data_from==1)
{
xy<-load_data_from_finnish_wiki()
print (xy)
}
if(load_data_from==2)
{
xy<-load_data_from_aggregated()
}
if(load_data_from==3)
{
xy<-download_solanpaa_finnish_data()
}
if(load_data_from==4)
{
xy<-lataa_thl_tapaukset_kuolleet()
}
names(xy)<-c("Dates","Cases")
select_datelimit_begin=as.Date(beginday1,format="%d/%m/%Y")
select_datelimit_end=as.Date(today1)
xy2<-xy[xy$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
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
dates<-paivat
- dates<-names1
I<-num1
- ceises <- setNames(dates, num)
ceises<-data.frame(dates, I)
incid<-I
- names(ceises)<-c("dates" "I")
- dates, I
- parametric si
config<-make_config( list(mean_si = 2.6,std_si = 1.5) )
res<-estimate_R(incid,method="parametric_si", config = config)
plot(res)
- plot(res, "R")
- uncertain si
- onfig <- make_config(list(mean_si = 2.6, std_mean_si = 1,
- min_mean_si = 1, max_mean_si = 4.2,
- std_si = 1.5, std_std_si = 0.5,
- min_std_si = 0.5, max_std_si = 2.5))
- es2 <- estimate_R(incid,method = "uncertain_si",config = config)
- lot(res2)
resr<-res$R
str(resr)
meanr<-resr$Mean
medianr<-resr$Median
quantile95<-resr$Quantile.0.95
quantile05<-resr$Quantile.0.05
quantile75<-resr$Quantile.0.75
quantile25<-resr$Quantile.0.25
meanr
daydexes<-resr$t_start
daydexes
dayss<-paivat[daydexes]
if(plottaa==1)
{
if(levylle==1)
{
plotname1<-paste0(polku, plotname)
svg(filename=plotname1, width=12, height=5, pointsize=12)
}
- plot(dayss, meanr, main="Koonaviruksen R0 Suomessa")
- plot(dayss, meanr, type="lines", col="black", lwd=3,
- main="Arvioitu koronaviruksen R0 Suomessa", xlab="Aika", ylab="R0",
- ylim=c(0.5,2), cex.lab=1.3, cex.axis=1.3, cex.main=1.3, cex.sub=1.3)
print (dayss)
dayss2=as.Date(dayss)
- plot(strptime(dayss2,"%Y-%m-%d"),meanr,type="l", xlab="Aika",ylab="R")
- plot( zoo(meanr,as.Date(dayss2,"%Y-%m-%d") ) )
time=as.POSIXct(dayss2)
y=meanr
plot(time,y,xaxt="n" ,
type="lines", col="black", lwd=3,
main="Arvioitu koronaviruksen R0 Suomessa", xlab="Kuukausi 2020-2021", ylab="Tartutusluku R0",
ylim=c(0.6,1.4), cex.lab=1.3, cex.axis=1.3, cex.main=1.3, cex.sub=1.3
)
axis.POSIXct(side=1,at=cut(time, breaks="month"),format="%b")
abline(h=1.0, col="#007f00", lty=2, lwd=3)
lines(time,meanr, col="black", lwd=4)
lines(time,medianr, col="#004f00", lwd=2)
lines(time,quantile95, col="red", lty=2)
lines(time,quantile05, col="blue", lty=2)
lines(time,quantile75, col="red", lty=1)
lines(time,quantile25, col="blue", lty=1)
if(levylle==1)
{
dev.off()
}
}
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.
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Date/Time | Thumbnail | Dimensions | User | Comment | |
---|---|---|---|---|---|
current | 08:20, 9 August 2021 | 1,080 × 450 (245 KB) | Merikanto (talk | contribs) | Upload | |
12:58, 30 May 2021 | 1,080 × 450 (219 KB) | Merikanto (talk | contribs) | Update | ||
09:35, 26 April 2021 | 1,080 × 450 (208 KB) | Merikanto (talk | contribs) | Päivitys | ||
12:29, 23 March 2021 | 1,080 × 540 (104 KB) | Merikanto (talk | contribs) | update | ||
14:13, 11 January 2021 | 1,080 × 540 (92 KB) | Merikanto (talk | contribs) | Update | ||
13:41, 3 December 2020 | 1,080 × 540 (98 KB) | Merikanto (talk | contribs) | Update | ||
11:54, 4 November 2020 | 1,080 × 540 (93 KB) | Merikanto (talk | contribs) | Update | ||
12:19, 18 September 2020 | 1,080 × 540 (85 KB) | Merikanto (talk | contribs) | Update | ||
13:49, 2 September 2020 | 1,080 × 540 (82 KB) | Merikanto (talk | contribs) | Update | ||
15:12, 14 August 2020 | 1,080 × 540 (80 KB) | Merikanto (talk | contribs) | Update |
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