Another option is https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide
Together with instruments from https://www.repidemicsconsortium.org/ Cheers Petr Here is some simple code library(EpiEstim) library(ggplot2) library(lubridate) library(incidence) library(distcrete) library(epitrix) library(readxl) mena <- c("Austria", "Czechia", "Germany", "Italy", "Japan", "Russia", "South_Korea", "Spain", "Sweden", "Taiwan", "United_States_of_America", "United_Kingdom") plot_Ri <- function(estimate_R_obj) { p_I <- plot(estimate_R_obj, "incid") + ggtitle(staty[vyber][i]) # plots the incidence p_SI <- plot(estimate_R_obj, "SI") # plots the serial interval distribution p_Ri <- plot(estimate_R_obj, "R") + ylim(c(0,5)) return(gridExtra::grid.arrange(p_I, p_Ri, ncol = 1)) } data <- read_excel("covid.xlsx") data <- as.data.frame(data) staty <- levels(factor(data[,7])) vyber <- which(staty %in% mena) staty[vyber] # covid.xlsx is downloaded data vyber <- which(staty %in% mena) vyber <- vyber[-6] staty[vyber] ddd <- vector("list", length=length(vyber)) pdf("grafy2.pdf") for (i in 1:length(vyber)) { temp <- data[data[,7]==staty[vyber][i],] temp$cas <- ymd(temp$dateRep) ooo <- order(temp$cas) temp <- temp[ooo,] temp<- temp[-1,] temp <- temp[-(1:min(which(temp$cases>0))-1),] head(temp) test <- temp[, c(12,5)] names(test) <- c("date", "I") test$I <- abs(test$I) inc <- rep(test$date, test$I) inci <- incidence(inc) peak <- find_peak(inci) fit <- incidence::fit(inci, split=peak) print(plot(inci, fit = fit)+ggtitle(staty[vyber][i])) ddd[[i]] <- rbind(fit$before$info$doubling.conf, fit$after$info$halving.conf) vysled <- estimate_R(test, method = "uncertain_si", config = make_config(list(mean_si = 4, std_mean_si = 2, min_mean_si = 1, max_mean_si = 8.4, std_si = 2.4, std_std_si = 1, min_std_si = 0.5, max_std_si = 4, n1 = 1000, n2 = 1000))) print(plot_Ri(vysled)) } dev.off() names(ddd) <- staty[vyber] ddd > -----Original Message----- > From: R-help <r-help-boun...@r-project.org> On Behalf Of Bernard Comcast > Sent: Monday, May 4, 2020 8:56 PM > To: James Spottiswoode <ja...@jsasoc.com> > Cc: r-help@r-project.org > Subject: Re: [R] COVID-19 datasets... > > Thanks, i will take a look > > Bernard > Sent from my iPhone so please excuse the spelling!" > > > On May 4, 2020, at 2:49 PM, James Spottiswoode <ja...@jsasoc.com> > wrote: > > > > Sure. COVID-19 Data Repository by the Center for Systems Science and > Engineering (CSSE) at Johns Hopkins University is available here: > > > > https://github.com/CSSEGISandData/COVID-19 > > > > All in csv fiormat. > > > > > >> On May 4, 2020, at 11:31 AM, Bernard McGarvey > <mcgarvey.bern...@comcast.net> wrote: > >> > >> Just curious does anyone know of a website that has data available in a > format that R can download and analyze? > >> > >> Thanks > >> > >> > >> Bernard McGarvey > >> > >> > >> Director, Fort Myers Beach Lions Foundation, Inc. > >> > >> > >> Retired (Lilly Engineering Fellow). > >> > >> ______________________________________________ > >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide > >> http://www.R-project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > James Spottiswoode > > Applied Mathematics & Statistics > > (310) 270 6220 > > jamesspottiswoode Skype > > ja...@jsasoc.com > > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
