In CDCgov/SaviR: ITF Situational Awareness and Visualization

knitr::opts_chunk$set(echo = TRUE)
library(SaviR)
library(dplyr)
library(tidyr)
library(tidyr)
library(lubridate)
library(ggplot2)
library(RcppRoll)

testing_df <- get_testing_long()
sunday_date <- floor_date(max(testing_df$date, na.rm = TRUE), "week")
testing_preferred_df <- get_testing(sunday_date)

Testing by Income Status

Aggregating to Income Level
Computing number of jurisdictions reporting per day
OWID turned off all testing data collection in July.

testing_by_income_14d <- testing_df %>%
  left_join(distinct(onetable, id, incomelevel_value, state_region), by = "id") %>%
  group_by(date, data_source, incomelevel_value) %>%
  summarize(
    n_reporting = sum(!new_tests_original %in% c(0, NA_real_)),
    new_tests = sum(new_tests_original, na.rm = TRUE)
  ) %>%
  group_by(data_source, incomelevel_value) %>%
  arrange(date) %>%
  mutate(
    n_reporting_14d = roll_median(n_reporting, n = 14, align = "right", na.rm = TRUE, fill = NA_real_),
    new_tests_14d = roll_median(new_tests, n = 14, align = "right", na.rm = TRUE, fill = NA_real_)
  ) %>%
  ungroup() %>%
  filter(
    !incomelevel_value %in% c("Not classified", NA_character_),
    date >= "2021-01-01",
    date <= sunday_date,
  ) %>%
  select(-new_tests, -n_reporting) %>%
  pivot_longer(-date:-incomelevel_value) %>%
  mutate(
    name = case_when(
      name == "n_reporting_14d" ~ "Countries Reporting",
      name == "new_tests_14d" ~ "New Tests Reported"
    ),
    incomelevel_value = factor(
      tools::toTitleCase(incomelevel_value),
      levels = c(
        "Low Income",
        "Lower Middle Income",
        "Upper Middle Income",
        "High Income"
      ),
      ordered = TRUE
    )
  )


testing_by_income_plot <- ggplot(testing_by_income_14d, aes(x = date, y = value, color = name, linetype = data_source)) +
  geom_line() +
  facet_grid(name ~ incomelevel_value, scales = "free_y", switch = "y") +
  scale_y_continuous(labels = scales::comma) +
  scale_x_date(
    date_labels = "%b\n%Y"
  ) +
  labs(
    title = "COVID-19 Testing Data Reporting, by World Bank Income Level",
    subtitle = "14-day median new tests reported and number of countries reporting",
    x = "Date of Report",
    y = "Value",
    color = "Metric",
    linetype = "Data Source"
  ) +
  theme_bw() + 
  theme(
    legend.position = "bottom"
  )

testing_by_income_plot