### Plots - new cases


model.au.fit.fn <- splinefun(all_days, model.au$fit)
model.au.fit.deriv <- model.au.fit.fn(all_days, deriv = 1)

model.au.upr.deriv <- model.au.fit.deriv + (model.au$upr - model.au$fit)
model.au.lwr.deriv <- model.au.fit.deriv - (model.au$fit - model.au$lwr)
model.au.lwr.deriv[model.au.lwr.deriv < 0] <- 0


# scaling factor for fixed elements on chart
sf = 800 / 1800
alphaPI = 0.1

p1 <- ggplot(data=au_covid, aes(x=day, y=new)) + 
	xlab("") + 
	ylab("Confirmed COVID-19 cases (Australia)") +

	geom_vline(xintercept=today, color = "grey") +

    geom_hline(yintercept=-150*sf) + 
	annotate("text", x=1, y=-200*sf, label="Jun 1") +
	annotate("text", x=15, y=-200*sf, label="Jun 15") +
	annotate("text", x=30+1, y=-200*sf, label="Jul 1") +
	annotate("text", x=30+15, y=-200*sf, label="Jul 15") +   
	annotate("text", x=30+31+1, y=-200*sf, label="Aug 1") +
	annotate("text", x=30+31+15, y=-200*sf, label="Aug 15") +
	annotate("text", x=30+31+31+1, y=-200*sf, label="Sep 1") +
	annotate("text", x=30+31+31+15, y=-200*sf, label="Sep 15") +
	annotate("text", x=30+31+31+30+1, y=-200*sf, label="Oct 1") +

	annotate("label", x=5, y=1800*sf, label="Simple moving average (7 days)", size=5.5, hjust=0) +
	annotate("text", x=5, y=1600*sf, label= paste(au_covid$date[today], "@", time, "GMT+10"), hjust=0) +

  
	geom_point(colour="white", size = 3.2) + 
	geom_point(colour="grey20", size = 2.8) +     

    # geom_ma(n=7, ma_fun=EMA, colour="dark green", linetype=1, size = 1) +
    geom_ma(n=7, colour="orange", linetype=1, size = 1) +
    # geom_smooth(colour="red3", fill="NA", method="gam") +
    # geom_line(aes(y=model.au.fit.deriv), colour="blue", size = 1, linetype=2) + 


    annotate("label", x=(today), y=-85*sf, label=au_covid$date[today], size=3) +
	coord_cartesian(ylim = c(-250*sf, 1800*sf), xlim = c(1,today+2)) 

p2 <- ggplot(data=au_covid, aes(x=day, y=new)) + 
	xlab("") + 
	ylab("") +

	geom_vline(xintercept=today, color = "grey") +

    geom_hline(yintercept=-150*sf) + 
	annotate("text", x=1, y=-200*sf, label="Jun 1") +
	annotate("text", x=15, y=-200*sf, label="Jun 15") +
	annotate("text", x=30+1, y=-200*sf, label="Jul 1") +
	annotate("text", x=30+15, y=-200*sf, label="Jul 15") +   
	annotate("text", x=30+31+1, y=-200*sf, label="Aug 1") +
	annotate("text", x=30+31+15, y=-200*sf, label="Aug 15") +
	annotate("text", x=30+31+31+1, y=-200*sf, label="Sep 1") +
	annotate("text", x=30+31+31+15, y=-200*sf, label="Sep 15") +
	annotate("text", x=30+31+31+30+1, y=-200*sf, label="Oct 1") +

	annotate("label", x=5, y=1800*sf, label="Exponential moving average (7 days)", size=5.5, hjust=0) +
	# annotate("text", x=5, y=1700*sf, label= paste(au_covid$date[today], "@", time, "GMT+10"), hjust=0) +

  
	geom_point(colour="white", size = 3.2) + 
	geom_point(colour="grey20", size = 2.8) +     

    geom_ma(n=7, ma_fun=EMA, colour="dark green", linetype=1, size = 1) +
    # geom_ma(n=7, colour="orange", linetype=1, size = 1) +
    # geom_smooth(colour="red3", fill="NA", method="gam") +
    # geom_line(aes(y=model.au.fit.deriv), colour="blue", size = 1, linetype=2) + 


    annotate("label", x=(today), y=-85*sf, label=au_covid$date[today], size=3) +
	coord_cartesian(ylim = c(-250*sf, 1800*sf), xlim = c(1,today+2))

p3 <- ggplot(data=au_covid, aes(x=day, y=new)) + 
	xlab("Days from Jun 1") + 
	ylab("Confirmed COVID-19 cases (Australia)") +

	geom_vline(xintercept=today, color = "grey") +

    geom_hline(yintercept=-150*sf) + 
	annotate("text", x=1, y=-200*sf, label="Jun 1") +
	annotate("text", x=15, y=-200*sf, label="Jun 15") +
	annotate("text", x=30+1, y=-200*sf, label="Jul 1") +
	annotate("text", x=30+15, y=-200*sf, label="Jul 15") +   
	annotate("text", x=30+31+1, y=-200*sf, label="Aug 1") +
	annotate("text", x=30+31+15, y=-200*sf, label="Aug 15") +
	annotate("text", x=30+31+31+1, y=-200*sf, label="Sep 1") +
	annotate("text", x=30+31+31+15, y=-200*sf, label="Sep 15") +
	annotate("text", x=30+31+31+30+1, y=-200*sf, label="Oct 1") +

	annotate("label", x=5, y=1800*sf, label="Generalised additive model", size=5.5, hjust=0) +
	# annotate("text", x=5, y=1700*sf, label= paste(au_covid$date[today], "@", time, "GMT+10"), hjust=0) +

  
	geom_point(colour="white", size = 3.2) + 
	geom_point(colour="grey20", size = 2.8) +     

    # geom_ma(n=7, ma_fun=EMA, colour="dark green", linetype=1, size = 1) +
    # geom_ma(n=7, colour="orange", linetype=1, size = 1) +
    geom_smooth(colour="red3", fill="NA", method="gam") +
    # geom_line(aes(y=model.au.fit.deriv), colour="blue", size = 1, linetype=2) + 


    annotate("label", x=(today), y=-85*sf, label=au_covid$date[today], size=3) +
	coord_cartesian(ylim = c(-250*sf, 1800*sf), xlim = c(1,today+2))

p4 <- ggplot(data=au_covid, aes(x=day, y=new)) + 
	xlab("Days from Jun 1") + 
	ylab("") +

	geom_vline(xintercept=today, color = "grey") +

    geom_hline(yintercept=-150*sf) + 
	annotate("text", x=1, y=-200*sf, label="Jun 1") +
	annotate("text", x=15, y=-200*sf, label="Jun 15") +
	annotate("text", x=30+1, y=-200*sf, label="Jul 1") +
	annotate("text", x=30+15, y=-200*sf, label="Jul 15") +   
	annotate("text", x=30+31+1, y=-200*sf, label="Aug 1") +
	annotate("text", x=30+31+15, y=-200*sf, label="Aug 15") +
	annotate("text", x=30+31+31+1, y=-200*sf, label="Sep 1") +
	annotate("text", x=30+31+31+15, y=-200*sf, label="Sep 15") +
	annotate("text", x=30+31+31+30+1, y=-200*sf, label="Oct 1") +

	annotate("label", x=5, y=1800*sf, label="Gompertz model projections", size=5.5, hjust=0) +
	# annotate("text", x=5, y=1700*sf, label= paste(au_covid$date[today], "@", time, "GMT+10"), hjust=0) +

  
	geom_point(colour="white", size = 3.2) + 
	geom_point(colour="grey20", size = 2.8) +     

    # geom_ma(n=7, ma_fun=EMA, colour="dark green", linetype=1, size = 1) +
    # geom_ma(n=7, colour="orange", linetype=1, size = 1) +
    # geom_smooth(colour="red3", fill="NA", method="gam") +
    geom_line(aes(y=model.au.fit.deriv), colour="blue", size = 1, linetype=1) + 


    annotate("label", x=(today), y=-85*sf, label=au_covid$date[today], size=3) +
	coord_cartesian(ylim = c(-250*sf, 1800*sf), xlim = c(1,today+2))

grid.arrange(p1, p2, p3, p4, nrow = 2)