# New Daily US Covid Cases & Deaths # Bob Agnew, raagnew1@gmail.com, raagnew.com library(graphics) end_date <- "Jul 23 2021" # Matched to end date on New York Times datasets options(scipen=999) # TOTAL US popn <- 328239523 # July 1 2019 per Census x <- read.csv("c:/COVID/US.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us.csv raw data) total_cases <- as.vector(x[-(1:37),2]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 59) tc <- ts(tc, frequency = 1, start = 59) total_cases <- ts(total_cases, frequency = 1, start = 58) pdf("c:/COVID/US_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily US Covid Cases from Feb 28 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")," Ending Daily Trend = ",formatC(round(tail(tc,1)),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total US Covid Cases % of Population from Feb 27 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:44),3]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 66) tc <- ts(tc, frequency = 1, start = 66) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 65 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 65 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 65 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 65 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily US Covid Deaths from Mar 6 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")," Ending Daily Trend = ",formatC(round(tail(tc,1)),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling US Covid Deaths % of Lagged Rolling US Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # SELECTED STATES # ARIZONA popn <- 7278717 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Arizona",] total_cases <- as.vector(x[-(1:47),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 74) tc <- ts(tc, frequency = 1, start = 74) total_cases <- ts(total_cases, frequency = 1, start = 73) pdf("c:/COVID/AZ_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Arizona Covid Cases from Mar 14 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Arizona Covid Cases % of Population from Mar 13 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:59),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 86) tc <- ts(tc, frequency = 1, start = 86) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 85 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 85 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 85 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 85 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Arizona Covid Deaths from Mar 26 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Arizona Covid Deaths % of Lagged Rolling Arizona Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # CALIFORNIA popn <- 39512223 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="California",] total_cases <- as.vector(x[-(1:33),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 59) tc <- ts(tc, frequency = 1, start = 59) total_cases <- ts(total_cases, frequency = 1, start = 58) pdf("c:/COVID/CA_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily California Covid Cases from Feb 28 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total California Covid Cases % of Population from Feb 27 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:49),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 75) tc <- ts(tc, frequency = 1, start = 75) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 74 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 74 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 74 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 74 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily California Covid Deaths from Mar 15 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling California Covid Deaths % of Lagged Rolling California Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # FLORIDA popn <- 21477737 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Florida",] total_cases <- as.vector(x[-(1:13),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 75) tc <- ts(tc, frequency = 1, start = 75) total_cases <- ts(total_cases, frequency = 1, start = 74) pdf("c:/COVID/FL_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Florida Covid Cases from Mar 15 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Florida Covid Cases % of Population from Mar 14 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:14),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 76) tc <- ts(tc, frequency = 1, start = 76) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 75 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 75 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 75 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 75 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Florida Covid Deaths from Mar 16 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Florida Covid Deaths % of Lagged Rolling Florida Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # ILLINOIS popn <- 12671821 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Illinois",] total_cases <- as.vector(x[-(1:43),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 68) tc <- ts(tc, frequency = 1, start = 68) total_cases <- ts(total_cases, frequency = 1, start = 67) pdf("c:/COVID/IL_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Illinois Covid Cases from Mar 8 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Illinois Covid Cases % of Population from Mar 7 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:54),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 79) tc <- ts(tc, frequency = 1, start = 79) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 78 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 78 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 78 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 78 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Illinois Covid Deaths from Mar 19 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Illinois Covid Deaths % of Lagged Rolling Illinois Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # MICHIGAN popn <- 9986857 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Michigan",] total_cases <- as.vector(x[-(1:1),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 72) tc <- ts(tc, frequency = 1, start = 72) total_cases <- ts(total_cases, frequency = 1, start = 71) pdf("c:/COVID/MI_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Michigan Covid Cases from Mar 12 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Michigan Covid Cases % of Population from Mar 11 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:9),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 80) tc <- ts(tc, frequency = 1, start = 80) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 79 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 79 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 79 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 79 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Michigan Covid Deaths from Mar 20 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Michigan Covid Deaths % of Lagged Rolling Michigan Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # NEW YORK popn <- 19453561 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="New York",] total_cases <- as.vector(x[-(1:1),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 63) tc <- ts(tc, frequency = 1, start = 63) total_cases <- ts(total_cases, frequency = 1, start = 62) pdf("c:/COVID/NY_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily New York Covid Cases from Mar 3 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("top",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total New York Covid Cases % of Population from Mar 2 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:13),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 75) tc <- ts(tc, frequency = 1, start = 75) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 74 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 74 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 74 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 74 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily New York Covid Deaths from Mar 15 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("top",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling New York Covid Deaths % of Lagged Rolling New York Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # NORTH CAROLINA popn <- 10488084 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="North Carolina",] total_cases <- as.vector(x[-(1:7),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 71) tc <- ts(tc, frequency = 1, start = 71) total_cases <- ts(total_cases, frequency = 1, start = 70) pdf("c:/COVID/NC_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily North Carolina Covid Cases from Mar 11 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total North Carolina Covid Cases % of Population from Mar 10 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:27),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 91) tc <- ts(tc, frequency = 1, start = 91) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 90 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 90 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 90 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 90 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily North Carolina Covid Deaths from Mar 31 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling North Carolina Covid Deaths % of Lagged Rolling North Carolina Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # TEXAS popn <- 28995881 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Texas",] total_cases <- as.vector(x[-(1:24),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 68) tc <- ts(tc, frequency = 1, start = 68) total_cases <- ts(total_cases, frequency = 1, start = 67) pdf("c:/COVID/TX_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Texas Covid Cases from Mar 8 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Texas Covid Cases % of Population from Mar 7 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:40),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 84) tc <- ts(tc, frequency = 1, start = 84) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 83 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 83 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 83 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 83 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Texas Covid Deaths from Mar 24 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Texas Covid Deaths % of Lagged Rolling Texas Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # PENNSYLVANIA popn <- 12801989 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Pennsylvania",] total_cases <- as.vector(x[,4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 67) tc <- ts(tc, frequency = 1, start = 67) total_cases <- ts(total_cases, frequency = 1, start = 66) pdf("c:/COVID/PA_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Pennsylvania Covid Cases from Mar 7 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Pennsylvania Covid Cases % of Population from Mar 6 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:14),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 81) tc <- ts(tc, frequency = 1, start = 81) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 80 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 80 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 80 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 80 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Pennsylvania Covid Deaths from Mar 21 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Pennsylvania Covid Deaths % of Lagged Rolling Pennsylvania Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # GEORGIA popn <- 10617423 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Georgia",] total_cases <- as.vector(x[-(1:10),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 73) tc <- ts(tc, frequency = 1, start = 73) total_cases <- ts(total_cases, frequency = 1, start = 72) pdf("c:/COVID/GA_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Georgia Covid Cases from Mar 13 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Georgia Covid Cases % of Population from Mar 12 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:21),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 84) tc <- ts(tc, frequency = 1, start = 84) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 83 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 83 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 83 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 83 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Georgia Covid Deaths from Mar 24 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Georgia Covid Deaths % of Lagged Rolling Georgia Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # OHIO popn <- 11689100 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Ohio",] total_cases <- as.vector(x[-(1:1),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 71) tc <- ts(tc, frequency = 1, start = 71) total_cases <- ts(total_cases, frequency = 1, start = 70) pdf("c:/COVID/OH_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Ohio Covid Cases from Mar 11 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Ohio Covid Cases % of Population from Mar 10 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:13),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 83) tc <- ts(tc, frequency = 1, start = 83) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 82 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 82 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 82 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 82 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Ohio Covid Deaths from Mar 23 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Ohio Covid Deaths % of Lagged Rolling Ohio Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # WISCONSIN popn <- 5822434 # July 1 2019 per Census x <- read.csv("c:/COVID/STATES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-states.csv raw data) x <- x[trimws(x[,2])=="Wisconsin",] total_cases <- as.vector(x[-(1:32),4]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 69) tc <- ts(tc, frequency = 1, start = 69) total_cases <- ts(total_cases, frequency = 1, start = 68) pdf("c:/COVID/WI_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Wisconsin Covid Cases from Mar 9 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Wisconsin Covid Cases % of Population from Mar 8 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:53),5]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 90) tc <- ts(tc, frequency = 1, start = 90) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 89 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 89 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 89 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 89 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Wisconsin Covid Deaths from Mar 30 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Wisconsin Covid Deaths % of Lagged Rolling Wisconsin Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # SELECTED COUNTIES # COOK, ILLINOIS popn <- 5150233 # July 1 2019 per Census x <- read.csv("c:/COVID/COUNTIES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-counties.csv raw data) x <- x[trimws(x[,2])=="Cook"&trimws(x[,3])=="Illinois",] total_cases <- as.vector(x[-(1:52),5]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 77) tc <- ts(tc, frequency = 1, start = 77) total_cases <- ts(total_cases, frequency = 1, start = 76) pdf("c:/COVID/COOK_IL_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Cook Cty IL Covid Cases from Mar 17 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Cook Cty IL Covid Cases % of Population from Mar 16 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:54),6]) k <- length(total_deaths) daily_deaths <- pmax(1,total_deaths[-1]-total_deaths[-k]) s <- ts(daily_deaths, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 79) tc <- ts(tc, frequency = 1, start = 79) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 78 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 78 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 78 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 78 + k - 172) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Deaths",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Cook Cty IL Covid Deaths from Mar 19 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Cook Cty IL Covid Deaths % of Lagged Rolling Cook Cty IL Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # BEXAR, TEXAS popn <- 2003554 # July 1 2019 per Census x <- read.csv("c:/COVID/COUNTIES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-counties.csv raw data) x <- x[trimws(x[,2])=="Bexar"&trimws(x[,3])=="Texas",] total_cases <- as.vector(x[-(1:40),5]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 84) tc <- ts(tc, frequency = 1, start = 84) total_cases <- ts(total_cases, frequency = 1, start = 83) pdf("c:/COVID/BEXAR_TX_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Bexar Cty TX Covid Cases from Mar 24 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Bexar Cty TX Covid Cases % of Population from Mar 23 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:40),6]) k <- length(total_deaths) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 83 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 83 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 83 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 83 + k - 172) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Bexar Cty TX Covid Deaths % of Lagged Rolling Bexar Cty TX Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # LAKE, ILLINOIS popn <- 696535 # July 1 2019 per Census x <- read.csv("c:/COVID/COUNTIES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-counties.csv raw data) x <- x[trimws(x[,2])=="Lake"&trimws(x[,3])=="Illinois",] total_cases <- as.vector(x[-(1:1),5]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 73) tc <- ts(tc, frequency = 1, start = 73) total_cases <- ts(total_cases, frequency = 1, start = 72) pdf("c:/COVID/LAKE_IL_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Lake Cty IL Covid Cases from Mar 13 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Lake Cty IL Covid Cases % of Population from Mar 12 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:17),6]) k <- length(total_deaths) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 88 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 88 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 88 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 88 + k - 172) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Lake Cty IL Covid Deaths % of Lagged Rolling Lake Cty IL Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # FLAGLER, FLORIDA popn <- 115081 # July 1 2019 per Census x <- read.csv("c:/COVID/COUNTIES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-counties.csv raw data) x <- x[trimws(x[,2])=="Flagler"&trimws(x[,3])=="Florida",] total_cases <- as.vector(x[-(1:7),5]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 89) tc <- ts(tc, frequency = 1, start = 89) total_cases <- ts(total_cases, frequency = 1, start = 88) pdf("c:/COVID/FLAGLER_FL_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Flagler Cty FL Covid Cases from Mar 29 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Flagler Cty FL Covid Cases % of Population from Mar 28 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:12),6]) k <- length(total_deaths) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 94 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 94 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 94 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 94 + k - 172) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Flagler Cty FL Covid Deaths % of Lagged Rolling Flagler Cty FL Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # CHEMUNG, NEW YORK popn <- 83456 # July 1 2019 per Census x <- read.csv("c:/COVID/COUNTIES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-counties.csv raw data) x <- x[trimws(x[,2])=="Chemung"&trimws(x[,3])=="New York",] total_cases <- as.vector(x[-(1:10),5]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 95) tc <- ts(tc, frequency = 1, start = 95) total_cases <- ts(total_cases, frequency = 1, start = 94) pdf("c:/COVID/CHEMUNG_NY_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Chemung Cty NY Covid Cases from Apr 4 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Chemung Cty NY Covid Cases % of Population from Apr 3 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:16),6]) k <- length(total_deaths) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 100 + k - 200) roll_deaths <- ts(pmax(0,total_deaths[-(1:28)] - total_deaths[-(173:200)]),frequency = 1, start = 100 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 100 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 100 + k - 172) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Chemung Cty NY Covid Deaths % of Lagged Rolling Chemung Cty NY Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off() # CUMBERLAND, PENNSYLVANIA popn <- 253370 # July 1 2019 per Census x <- read.csv("c:/COVID/COUNTIES.csv",header=TRUE) # From github.com/nytimes/covid-19-data (us-counties.csv raw data) x <- x[trimws(x[,2])=="Cumberland"&trimws(x[,3])=="Pennsylvania",] total_cases <- as.vector(x[-(1:12),5]) k <- length(total_cases) daily_cases <- pmax(1,total_cases[-1]-total_cases[-k]) s <- ts(daily_cases, frequency = 7, start = 1) logs <- ts(log(s), frequency = 7, start = 1) t <- stl(logs,"per") tc <- exp(t$time.series[,2]) s <- ts(s, frequency = 1, start = 86) tc <- ts(tc, frequency = 1, start = 86) total_cases <- ts(total_cases, frequency = 1, start = 85) pdf("c:/COVID/CUMBERLAND_PA_COVID_CASES_AND_DEATHS.pdf",width=10,height=7,onefile=TRUE) ts.plot(s,tc,gpars=list(lty=rep(1,2),lwd=rep(2,2),ylab="New Daily Covid Cases",xlab="Days since 2019",tck=1,col=c("blue","red"),main=paste0("New Daily Cumberland Cty PA Covid Cases from Mar 26 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) legend("topleft",bty="n",lty=rep(1,2),lwd=rep(2,2),col=c("blue","red"),legend=c("Actual","Trend")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) ts.plot(100*total_cases/popn,gpars=list(lty=1,lwd=2,ylab="Total Covid Cases % of Population",xlab="Days since 2019",tck=1,col="blue",main=paste0("Total Cumberland Cty PA Covid Cases % of Population from Mar 25 2020 to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Cases = ",formatC(tail(total_cases,1),format="d",big.mark=",")),side=3) total_deaths <- as.vector(x[-(1:44),6]) k <- length(total_deaths) total_deaths <- ts(tail(total_deaths,200), frequency = 1, start = 117 + k - 200) roll_deaths <- ts(total_deaths[-(1:28)] - total_deaths[-(173:200)],frequency = 1, start = 117 + k - 172) total_cases <- ts(tail(total_cases,221)[-(201:221)], frequency = 1, start = 117 + k - 200) # Cases lagged by 21 days roll_cases <- ts(total_cases[-(1:28)] - total_cases[-(173:200)],frequency = 1, start = 117 + k - 172) ts.plot(100*roll_deaths/roll_cases,gpars=list(lty=1,lwd=2,ylab="28-Day Rolling Covid Deaths % of Rolling Covid Cases lagged 21 Days",xlab="Days since 2019",tck=1,col="blue",main=paste0("Rolling Cumberland Cty PA Covid Deaths % of Lagged Rolling Cumberland Cty PA Covid Cases to ",end_date),sub="Data from New York Times : github.com/nytimes/covid-19-data")) mtext(paste0("Total Deaths = ",formatC(tail(total_deaths,1),format="d",big.mark=",")),side=3) dev.off()