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jbkunst/script.r

Created February 17, 2020 22:00
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script.r
library(tidyverse)
library(lubridate)
library(highcharter)
confirmed <- read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv")
get_data <- function(url = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Deaths.csv"){
data_wide <- read_csv(url)
data_long <- data_wide %>%
gather(date, value, -`Province/State`, -`Country/Region`, -Lat, -Long) %>%
rename_all(str_to_lower) %>%
rename_all(str_replace_all, "/", "_") %>%
mutate(date = mdy(str_extract(date, "[0-9]+/[0-9]+/[0-9]+"))) %>%
group_by(province_state, country_region, lat, long, date) %>%
summarise(value = max(value)) %>%
ungroup() %>%
arrange(province_state, date) %>%
mutate(value = ifelse(value == 0, NA, value))
dmap <- data_long %>%
group_by(province_state, country_region, lat, long) %>%
summarise(sequence = list(value)) %>%
ungroup()
dmap
}
confmd <- get_data("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv")
deaths <- get_data("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Deaths.csv")
rcvred <- get_data("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Recovered.csv")
data <- list(
confmd,
deaths,
rcvred
) %>%
map2_df(
c("confirmed", "deaths", "recovered"),
~ mutate(.x, category = .y)
) %>%
unnest(sequence)
dates <- data %>%
distinct(date) %>%
arrange(date) %>%
pull()
dates <- confirmed %>%
select(5:last_col()) %>%
names() %>%
mdy()
auxseq <- data %>%
summarise(max(sequence, na.rm = TRUE)) %>%
pull() %>%
rep(times = length(dates))
aux <- tibble(
province_state = "false",
name = "false",
lat = NA,
long = NA,
sequence = list(auxseq)
)
aux
hcmap(showInLegend = FALSE) %>%
hc_add_series(
data = confmd,
type = "mapbubble",
name= "Confirmed",
hcaes(lat = lat, lon = long, size = sequence, name = paste(country_region, province_state)),
color = "yellow"
) %>%
hc_add_series(
data = deaths,
type = "mapbubble",
name= "Deaths",
hcaes(lat = lat, lon = long, size = sequence, name = paste(country_region, province_state)),
color = "red"
) %>%
hc_add_series(
data = rcvred,
type = "mapbubble",
name= "Recovered",
hcaes(lat = lat, lon = long, size = sequence, name = paste(country_region, province_state)),
color = "green"
) %>%
hc_add_series(
data = auxiliar,
type = "mapbubble",
name= "auxiliar",
hcaes(lat = lat, lon = long, size = sequence, name = province_state),
enableMouseTracking= FALSE,
color = "transparent",
showInLegend = FALSE
) %>%
hc_mapNavigation(enabled = TRUE) %>%
hc_plotOptions(
bubble = list(
minSize = 0,
maxSize = 20,
sizeBy = "area"
)
) %>%
hc_motion(
enabled = TRUE,
series = c(1:4),
labels = dates,
autoPlay = FALSE,
magnet = list(step = 1),
updateInterval = 400
) %>%
hc_tooltip(useHTML = TRUE)
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