SF COVID ICU animation 2021-12-31

library(httr); library(jsonlite)
library(tidyverse); library(lubridate)
library(gganimate); library(ggtext)


sf_hosp <- GET("https://data.sfgov.org/resource/nxjg-bhem.json?$limit=999999")
sf_hosp$content %>% 
  rawToChar %>% 
  fromJSON %>% 
  mutate(patientcount = as.numeric(patientcount),
         reportdate = as.Date(reportdate)) %>%
  filter(covidstatus == "COVID+") %>%
  arrange(reportdate) %>%
  mutate(dphcategory = forcats::fct_rev(dphcategory)) %>%
  group_by(dphcategory) %>%
  mutate(avg = slider::slide_index_dbl(patientcount, reportdate,
                                       mean, .before = lubridate::days(6))) -> sf_hosp_clean
 

  sf_hosp_clean %>%
    select(-patientcount, -data_loaded_at) %>%
    tidyr::pivot_wider(names_from = dphcategory, values_from = avg) %>%
    mutate(ratio = ICU / `Med/Surg`) %>%
    mutate(era = case_when(
      reportdate <= ymd(20200621) ~ "First wave<br><i style='color:#BBBBBB'>Mar-Jun '20</i>",
      reportdate <= ymd(20201021) ~ "Summer 2020<br><i style='color:#BBBBBB'>Jul-Oct '20",
      reportdate <= ymd(20210401) ~ "Winter '20-21<br><i style='color:#BBBBBB'>Nov'20-Mar'21",
      reportdate <= ymd(20210702) ~ "pre-Delta<br><i style='color:#BBBBBB'>Apr-Jul '21",
      reportdate <= ymd(20211129) ~ "Delta<br><i style='color:#BBBBBB'>Aug-Nov '21",
      TRUE ~ "Omicron<br><i style='color:#BBBBBB'>Dec '21 - ??"
    ) %>% forcats::fct_reorder(reportdate)) %>%
    group_by(era) %>%
    mutate(era_stage = row_number()) %>% 
    ungroup() -> sf_hosp_clean_anim
    
animate(
  sf_hosp_clean_anim %>%
    ggplot(aes( `Med/Surg`, ICU)) +
    geom_path(data  = . %>% select(-era, -era_stage), color = "gray80", alpha = 1) +
    geom_path(aes(color = era), size = 1.2, show.legend = FALSE) +
    geom_point(aes(color = era), size = 2, show.legend = FALSE) +
  facet_wrap(~era) +
    expand_limits(y = 0) +
    scale_x_continuous(minor_breaks =  NULL) +
    scale_y_continuous(minor_breaks = NULL) +
    labs(y = "# in Intensive Care",
         x = "# in Acute Care",
         title = "San Francisco COVID+ going to ICUs less than in prior waves",
         caption = "Data through 2021-12-31\nSource: SFDPH, via https://sf.gov/data/covid-19-hospitalizations") +
    theme_minimal(base_size = 24) +
    ggthemes::scale_color_tableau(direction = -1) +
    theme(strip.text = element_markdown(),
          panel.grid = element_line(size = 0.5),
          plot.title = element_text(size = 23),
          plot.caption = element_text(color = "gray70", size = 16)) +
    transition_reveal(era_stage) +
    shadow_wake(wake_length = 1, alpha = 0.8, exclude_layer = 2, wrap = FALSE), 
  fps = 20, duration = 8, width = 800, height = 600, device = "ragg_png", 
  start_pause = 20, end_pause = 20, renderer = gifski_renderer(file = "SF_beds_20211231.gif"))