R0plot.R

library(dplyr)
library(ggplot2); theme_set(theme_bw())

library(shellpipes)
rpcall("R0plot.Rout .pipestar R0plot.R slow/egf_R0.rda series.tsv")
startGraphics()

loadEnvironments()

## Doing vaccination correction here
dat <- (egf_gi2
	|> left_join(tsvRead(),by=c("loc"="varname"))
	|> mutate(NULL
	, est = est/(1-vac)
	, lwr = lwr/(1-vac)
	, upr = upr/(1-vac)
	, loc_final = ifelse(loc == "Tokyo1", "Tokyo",loc)
	, loc_final = ifelse(loc_final == "Tokyo2", "Tokyo",loc_final)
	, loc_final = paste0(loc_final, "\n", year)
	, loc_final = forcats::fct_reorder(loc_final,est,.fun = mean, .na_rm=FALSE))
)

print(dat)

gg <- (ggplot(filter(dat,method=="Logistic"), aes(y=loc_final))
    + geom_pointrange(aes(xmin=lwr, x = est, xmax=upr, color=phase)
                    , pch = 17
                    , position = position_dodge(width=-0.4)
	)
    + scale_color_manual(values=c("black","red", "orange"))
    + labs(x = "R0", y = NULL)
)

print(gg)

print(gg + coord_cartesian(ylim=c(0,3)) + coord_flip(ylim=c(0,3)))


rdsSave(gg)