plot-weekdays.R

# need to do this within the repo at
# https://github.com/gadenbuie/covid19-florida

library(dplyr, warn.conflicts = FALSE)
library(tidyr, warn.conflicts = FALSE)
library(readr, warn.conflicts = FALSE)
library(lubridate, warn.conflicts = FALSE)
library(ggplot2, warn.conflicts = FALSE)
library(purrr, warn.conflicts = FALSE)
library(ggiraph, warn.conflicts = FALSE)
source(here::here("R/combine-sources.R"))

fix_late_reporting <- function(x, start, end, adjusted) {
  return(x)
  dplyr::mutate(
    x,
    timestamp = dplyr::if_else(
      timestamp >= lubridate::ymd_hm(start, truncated = 2) &
        timestamp <= lubridate::ymd_hm(end, truncated = 2),
      lubridate::ymd_hm(adjusted, truncated = 2),
      timestamp
    )
  )
}

line_list <- readr::read_csv("data/covid-19-florida_arcgis_line-list.csv", guess_max = 1e5)
dash <- readr::read_csv("data/covid-19-florida_arcgis_summary.csv", guess_max = 1e5) %>%
  fix_late_reporting("2020-05-07 13", "2020-05-07 23", "2020-05-07 12:59")

# Test summary import -----------------------------------------------------

testing_summary_dash <- read_csv("data/covid-19-florida_dash_summary.csv") %>%
  mutate_at("timestamp", lubridate::ymd_hms) %>%
  fix_late_reporting("2020-05-07 13", "2020-05-07 23", "2020-05-07 12:59")

test_summary <-
  combine_scraped_and_api_data(testing_summary_dash, dash)

g_test_changes <-
  test_summary %>% 
  select(day, positive, deaths, pending) %>% 
  filter(!is.na(positive)) %>% 
  arrange(day) %>% 
  mutate(
    positive = positive - lag(positive),
    deaths = deaths - lag(deaths),
    complete = if_else(day == today(), "today", "past")
  ) %>% 
  filter(!is.na(positive)) %>% 
  select(day, complete, positive, deaths) %>% 
  pivot_longer(cols = c(positive, deaths), names_to = "status") %>% 
  mutate_at(vars(status), tools::toTitleCase) %>% 
  mutate_at(vars(status), factor, levels = c("Positive", "Deaths")) %>% 
  mutate(weekday = wday(day, label = TRUE)) %>%
  ggplot() +
  aes(day, value) +
  geom_col_interactive(aes(alpha = complete, fill = status, tooltip = weekday, data_id = weekday), width = 1) +
  geom_line(
    data = . %>%
      group_by(status) %>%
      mutate_at(vars(value), ~ slider::slide_dbl(.x, mean, .before = 7)),
    aes(color = status),
    size = 1
  ) +
  labs(
    x = NULL, y = NULL,
    caption = glue::glue(
      "Last update: {max(test_summary$timestamp)}",
      "Source: Florida DOH", 
      "github.com/gadenbuie/covid19-florida",
      .sep = "\n"
    )
  ) +
  ggtitle(
    label = "Daily Change in Testing",
    subtitle = "Florida COVID-19"
  ) +
  scale_alpha_manual(
    values = c(past = 1, today = 0.33),
    guide = FALSE
  ) +
  scale_color_manual(
    values = c(Pending = "#63768d", Positive = "#ec4e20", Deaths = "#440154"),
    guide = FALSE
  ) +
  scale_fill_manual(
    # values = c(Pending = "#63768d", Positive = "#ec4e20", Deaths = "#440154"), 
    values = c(Pending = "#63768d", Positive = "#f7b8a5", Deaths = "#b499ba"),
    guide = FALSE
  ) +
  theme_minimal(base_size = 14) +
  scale_x_date(date_breaks = "1 month", expand = expand_scale(add = 0.5), date_labels = "%B") +
  scale_y_continuous(expand = expansion()) +
  coord_cartesian(clip = "off") +
  theme(
    plot.margin = margin(0.5, 0.5, 0.5, 0.5, unit = "lines"),
    plot.subtitle = element_text(margin = margin(b = 1.25, unit = "lines")),
    plot.caption = element_text(color = "#444444"),
    panel.border = element_rect(color = "#dddddd", fill = NA),
    strip.text = element_text(face = "bold"),
    axis.title.y = element_text(angle = 0, hjust = 1),
    # panel.grid.major.x = element_blank(),
    panel.grid.minor.x = element_blank(),
    panel.grid.minor.y = element_blank()
  ) + 
  facet_wrap(~ status, scales = "free_y")

girafe(ggobj = g_test_changes) %>%
  girafe_options(
    opts_tooltip(opacity = .7)
  )