corona/COVID19.Rmd at master · nicebread/corona · GitHub

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---
title: ""
output: pdf_document
geometry: paperheight=8in, paperwidth=11in
params:
  dat_selection: NA
  logScale: NA
  start_cumsum: NA
  datasource: NA
  current_data_date: NA
  percGrowth: NA
  offset: NA
  max_day_since_start: NA
  showReferenceLine: NA
  target: NA
  smoother_span: NA
  smoother_se: NA
  estRange: NA

---

\pagenumbering{gobble}

```{r echo=FALSE, fig.width = 10.4, fig.height=7.5, message=FALSE, warning=FALSE}

growth <- function(x, percGrowth=33, intercept=100) {intercept*(1 + percGrowth/100)^(x-1)}


  target_label <- switch(params$target,
  			"cum_cases" = "confirmed cases",
  			"cum_cases_per_100000" = "confirmed cases",
  			"cum_deaths_per_100000" = "confirmed deaths",
  			"cum_deaths" = "confirmed deaths")

  y_label_0 <- switch(params$target,
			"cum_cases" = "Cumulative number of confirmed cases",
			"cum_cases_per_100000" = "Cumulative number of confirmed cases, per 100,000",
			"cum_deaths_per_100000" = "Cumulative number of confirmed deaths, per 100,000",
			"cum_deaths" = "Cumulative number of confirmed deaths",
			"dailyGrowth" = "Daily growth of confirmed cases in %"
		)

  y_label <- paste0(y_label_0, ifelse(params$logScale == TRUE, " (log scale)", ""))

  # For log scale: deaths +1 to avoid log error
	if (params$target %in% c("cum_deaths", "cum_deaths_per_100000")) {
		real_target <- paste0(params$target, "_noZero")
	} else {
		real_target <- params$target
	}

  if(!is.null(params$dat_selection$day_since_start)){ # This is to check if any countries are selected

  	if ('state' %in% names(params$dat_selection)) {
			p1 <- ggplot(params$dat_selection, aes_string(x="day_since_start", y=real_target, color='state')) +
			  geom_label_repel(aes(label = state_label), nudge_x = 1, na.rm = TRUE)
			startupflag_state <<- FALSE # Once one graph of states has been completed, turn off startup flag for states
		} else {
			p1 <- ggplot(params$dat_selection, aes_string(x="day_since_start", y=real_target, color='country')) +
			            geom_label_repel(aes(label = country_label), nudge_x = 1, na.rm = TRUE)
		}

    # if estimation range is restricted: show grey rect
		if ((params$estRange[1]>1 | params$estRange[2]< params$max_day_since_start) & params$showReferenceLine == TRUE) {
			p1 <- p1 +
			annotate(geom="rect", xmin=params$estRange[1], xmax=min(params$estRange[2], params$max_day_since_start ), ymin=params$start_cumsum, ymax=max(params$dat_selection[, params$target])*1.05, fill="azure2", alpha=.3) +
			annotate(geom="text", x=params$estRange[1], y=max(params$dat_selection[, params$target]), label="Curve estimated based on values in the shaded rectangle", hjust=0, size=3)
		}

	if (params$target == "dailyGrowth") {
			p1 <- p1 + geom_smooth(span=params$smoother_span, se=params$smoother_se)
		} else {
			p1 <- p1 +
				geom_point() +
				geom_line()
		}

    p1 <- p1 +	scale_color_discrete(guide = FALSE) +
			theme_bw() +
			labs(
				title = paste0("Visualization based on data from ", params$datasource, ". "),
			  subtitle = paste0("Data set from ", params$current_data_date),
			  caption = ifelse(params$target %in% c("cum_cases_per_100000", "cum_deaths_per_100000", "cum_deaths"),
			                   "Source: http://shinyapps.org/apps/corona/ \n Adjusted cumulative cases per capita: 100,000 x (cumulative cases / population)",
			                   "Source: http://shinyapps.org/apps/corona/"),
			  x = paste0("Days since ", params$start_cumsum, "th case"), y = y_label)


  if (params$logScale == TRUE) {
		  p1 <- p1 + coord_trans(y = "log10")
		}
		if (params$target == "cum_cases") {
			p1 <- p1 + scale_y_continuous(breaks=c(100, 200, 500, 1000, 2000, 5000, 10000, 20000))
		}
		if (params$target %in% c("cum_cases_per_100000", "cum_deaths_per_100000", "cum_deaths")) {
			p1 <- p1 + scale_y_continuous()
		}
		if (params$target == "dailyGrowth") {
			p1 <- p1 + scale_y_continuous(labels = scales::percent_format(accuracy = 1))
		}

		if (params$showReferenceLine == TRUE) {
		  p1 <- p1 +
		    stat_function(fun = growth, args=list(percGrowth=params$percGrowth, intercept=params$offset), color="black", linetype="dashed", xlim=c(max(params$estRange[1], min(params$dat_selection$day_since_start)), min(params$estRange[2], params$max_day_since_start ))) +
				stat_function(fun = growth, args=list(percGrowth=params$percGrowth, intercept=params$offset), color="grey80", linetype="dotted") +
		    annotate(label=paste0(params$percGrowth, "% growth rate"), x=params$max_day_since_start , y=growth(params$max_day_since_start+1, percGrowth=params$percGrowth, intercept=params$offset), geom="text", hjust=1)
		}

p1

  } else {
  ggplot()
}

# print(paste0("Using target variable ", real_target))
# print(summary(params$dat_selection$cum_deaths_per_100000_noZero))

```