Visualize vaccine uptake in Saskatchewan using the Government's official numbers

sk_vaccine.R

library(tidyverse)
library(RcppRoll)
library(rvest)


# Create temporary directory
tmp_dir <- tempdir()
file_path <- paste0(tmp_dir, "/vaccine_sk.csv")

# Download file
# Note: the filename changes everyday, so scrape the URL
base_url <- "https://dashboard.saskatchewan.ca"
file_url <- paste0(base_url, "/health-wellness/covid-19-vaccines/vaccines") |> 
    read_html() |> 
    html_nodes("div.indicator-export a") |> 
    html_attr("href") |> 
    str_subset("csv$")

download.file(paste0(base_url, file_url),
              file_path)

# Read-in data
# Note: There are a lot of empty rows at the beginning, and therefore
#       we need to read in a lot of rows to guess the data types
data <- read_csv(file_path, guess_max = 7500)

# Sum over all regions and compute rolling averages using RcppRoll
# Note: You may need to change the pipe operator if using older version of R
data <- data |> 
    group_by(Date) |> 
    summarise(first_dose = sum(`New First Vaccine Doses`, na.rm = TRUE),
              full_dose = sum(`New Fully Vaccinated`, na.rm = TRUE),
              total_dose = first_dose + full_dose) |>
    mutate(first_dose = roll_mean(first_dose, n = 7,
                                  fill = NA,
                                  align = "right"),
           full_dose = roll_mean(full_dose, n = 7,
                                  fill = NA,
                                  align = "right"),
           total_dose = roll_mean(total_dose, n = 7,
                                  fill = NA,
                                  align = "right")) |> 
    filter(first_dose + full_dose > 0) # Remove empty rows at the top

# Create long dataset for plotting separate lines
data |> 
    pivot_longer(!Date, names_to = "type",
                 values_to = "count") |>
    mutate(type = factor(type, 
                         levels = c("first_dose", "full_dose", "total_dose"),
                         labels = c("First dose", "Fully vacc.", "Total"))) |> 
    ggplot(aes(x = Date, y = count,
               colour = type)) +
    geom_line() +
    theme_bw() +
    scale_colour_manual(name = "", values = c(colorspace::qualitative_hcl(2), "black")) +
    theme(legend.position = "top") +
    labs(caption = "Source: https://dashboard.saskatchewan.ca/health-wellness") +
    xlab("") + ylab("Number of doses (7-day avg)") +
    scale_y_continuous(labels = scales::comma)

The output from the code above (ran on 2021-08-04 12:07:57 MDT):