In the previous post I showed how to use data from Johns Hokins to create a graph of the deaths from Covid-19.

In this post, I’ll show how we can use data from UNESCO to mark the dates when schools closed.

First, we need to run the previous .R script and use read.csv() to load the data.

# Run the previous .R script 
source('COVID_DEATHS_GRAPHS.R')

# Load data 
data_raw <- read.csv('https://en.unesco.org/sites/default/files/covid_impact_education.csv', as.is = TRUE)

As before, there are various data-management steps. This time we need to change the names of the UK and the US to match the previous dataset, and only keep the countries we want to use.

# Re-name UK and US 
data_raw$Country[data_raw$Country=='United Kingdom of Great Britain and Northern Ireland'] <- 'United Kingdom'

data_raw$Country[data_raw$Country=='United States of America'] <- 'US'

# Keep only the selected countries 
schools <- data_raw[data_raw$Country %in% countries &
                    data_raw$Scale == 'National', ]

We can now add the data to the plot from before. The code from the previous plot is repeated below, with an additional few steps in the for() loop that produced the trend lines.

# Start with an 'empty' plot of Italy 
plot_data <- data[data$Group.1=='Italy', ]

plot(plot_data$x, type = 'n', 
     log = 'y', # y-axis is on the log scale 
     bty = 'n', # no border around the plot 
     xlim = c(1,(nrow(plot_data)+4)),
     axes = FALSE, bg='gray80',
     xlab='Days after 10 confirmed deaths',
     ylab='Confirmed deaths (log scale)',
     sub = 'N.B. US has not closed schools; Japan closed before 10 deaths',
     cex.sub=.6,
     cex.lab=.7)

# Add gridlines 
grid(nx = NULL, ny = NULL, col = "lightgray", lty = "dotted", lwd = par("lwd"), equilogs = F)

# Add each of the other countries 
for (country in countries){
  plot_data <- data[data$Group.1 == country,]
  # Plot the lines 
  lines(c(1:nrow(plot_data)), plot_data$x, 
        col=cols[which(countries==country)])
  # Add the School closures
  # Skip the US, because schools haven't closed 
  if (country != 'US'){
    # Create marker for when schools first closed
    closed <- schools[schools$Country==country,]
    closed <- data.frame(date = as.Date(closed[1,1],
                         '%d/%m/%Y'), now=1)
    
    # Merge the marker with the plot data 
    plot_data_s <- merge(plot_data, closed,
                         by.x='Group.2',
                         by.y='date',
                         all.x=T)
    
    # Identify day and deaths when schools closed
    closed <- c(which(plot_data_s$now==1),
          plot_data_s$x[which(plot_data_s$now==1)])
    
    # Add the lines 
    lines(x=c(closed[1],closed[1]),
          y=c(5, closed[2]),
          col=cols[which(countries==country)],
          lty=2, lwd=.7)
    lines(x=c(0,closed[1]),
          y=c(closed[2], closed[2]),
          col=cols[which(countries==country)],
          lty=2, lwd=.7)
  }
  # Add a label
  text(x=nrow(plot_data), y=max(plot_data$x),
       label=paste0(country,' (',nrow(plot_data),' days)'), 
       pos=4, offset=.1, cex=.6, font=2,
       col=cols[which(countries==country)])
}

# Add the axes 
axis(1, lwd=0, cex.axis=.7)
axis(2, lwd=0, las=1, cex.axis=.7)

# Add titles
mytitle = "Covid-19 deaths"
mysubtitle = "Arranged by number of days since 10 or more deaths"
mtext(side=3, line=2, at=-0.07, adj=0, cex=1, mytitle)
mtext(side=3, line=1, at=-0.07, adj=0, cex=0.7, mysubtitle)

# Add a legend 
legend(x='bottomright', 
       legend=c('Schools closed'), lty=2,
       bty='n', cex=.7)